GenPlay, Einstein Genome Analyzer - User contributions [en]

Library

2017-01-03T16:53:22Z

Julien:

The library contains a few useful files for human and mouse genomes to get you started, including gene annotations and a few data files.

You can easily load data file downloaded from the [http://genome.ucsc.edu/cgi-bin/hgTables table browser of the UCSC genome browser] in GenPlay. Just select a table, set the output format to BED and click on the "get output" button.

If you have files of general interest that you would like to make available to other GenPlay users, please send them [mailto:julien.lajugie@einstein.yu.edu?Subject=GenPlay%20library here]

=== Links to the library ===

*Human
**[http://genplay.net/library/Human/hg18 hg18]
**[http://genplay.net/library/Human/hg19 hg19]
**[http://genplay.net/library/Human/hg38 hg38]
*mouse
**[http://genplay.net/library/Mouse/mm8 mm8]
**[http://genplay.net/library/Mouse/mm9 mm9]

Library

2016-12-23T23:31:50Z

Julien:

The library contains a few useful files for human and mouse genomes to get you started, including gene annotations and a few data files.

You can easily load data file downloaded from the [http://genome.ucsc.edu/cgi-bin/hgTables table browser of the UCSC genome browser] in GenPlay. Just select a table, set the output format to BED and click on the "get output" button.

If you have files of general interest that you would like to make available to other GenPlay users, please send them [mailto:julien.lajugie@einstein.yu.edu?Subject=GenPlay%20library here]

=== Links to the library ===

*Human
**[http://genplay.net/library/Human/hg18 hg18]
**[http://genplay.net/library/Human/hg19 hg19]
**[http://genplay.net/library/Human/hg38 hg38]
**[http://genplay.net/library/Human/Multi-Genome Multi-Genome]
*mouse
**[http://genplay.net/library/Mouse/mm8 mm8]
**[http://genplay.net/library/Mouse/mm9 mm9]

Library

2016-12-23T18:50:13Z

Julien:

The library contains a few useful files for human and mouse genomes to get you started, including gene annotations and a few data files.

You can easily load data file downloaded from the [http://genome.ucsc.edu/cgi-bin/hgTables table browser of the UCSC genome browser] in GenPlay. Just select a table, set the output format to BED and click on the "get output" button.

If you have files of general interest that you would like to make available to other GenPlay users, please send them [mailto:julien.lajugie@einstein.yu.edu?Subject=GenPlay%20library here]

=== Links to the library ===

*Human
**[http://www.genplay.net/library/Human/hg18 hg18]
**[http://www.genplay.net/library/Human/hg19 hg19]
**[http://www.genplay.net/library/Human/hg38 hg38]
**[http://www.genplay.net/library/Human/Multi-Genome/ Multi-Genome]
*mouse
**[http://www.genplay.net/library/Mouse/mm8 mm8]
**[http://www.genplay.net/library/Mouse/mm9 mm9]

Library

2016-12-23T18:49:42Z

Julien:

The library contains a few useful files for human and mouse genomes to get you started, including gene annotations and a few data files.

You can easily load data file downloaded from the [http://genome.ucsc.edu/cgi-bin/hgTables table browser of the UCSC genome browser] in GenPlay. Just select a table, set the output format to BED and click on the "get output" button.

If you have files of general interest that you would like to make available to other GenPlay users, please send them [mailto:julien.lajugie@einstein.yu.edu?Subject=GenPlay%20library here]

=== Links to the library ===

*Human
**[http://www.genplay.net/library/Human/hg18 hg18]
**[http://www.genplay.net/library/Human/hg19 hg19]
**[http://www.genplay.net/library/Human/hg38 hg38]
**[http://genplay.net/library/Human/Multi-Genome/ Multi-Genome]
*mouse
**[http://www.genplay.net/library/Mouse/mm8 mm8]
**[http://www.genplay.net/library/Mouse/mm9 mm9]

News

2016-12-23T18:48:34Z

Julien:

== Updates ==
'''06-14-2016 - ''' New article posted in Projects section.

'''06-01-2016 - ''' [http://onlinelibrary.wiley.com/doi/10.1002/ajh.24444/abstract Article in Memory of Ron Nagel] [http://genplay.net/library/projects/pdf/Bouhassira_et_al-2016-American_Journal_of_Hematology pdf]

'''05-05-2015 - ''' New article posted in Projects section.

'''01-05-2015 - ''' New article posted in Projects section.

'''09-02-2014 - ''' Check out tutorial on how to visualize all changes between hg19 to hg38 in GenPlay Multi-Genome Bioinformatics paper.

'''09-02-2014 - ''' New GenPlay application note describing GenPlay multi-genome functions published in Bioinformatics. Access paper [http://bioinformatics.oxfordjournals.org/content/early/2014/08/31/bioinformatics.btu588.short?rss=1| here. ]

'''06-30-2014 - ''' [[Release_Notes#GenPlay_v1.1.0|GenPlay v1.1.0]] released. The version 1.1.0 is out. GenPlay can now be [[Downloads|installed]] on Windows, Mac and Linux. Project and track files can be double clicked from a file explorer. Tracks can be dragged and dropped between instances of GenPlay, or between GenPlay and an explorer.

'''01-09-2014 - ''' [[Release_Notes#GenPlay_v996|GenPlay v996]] released. We corrected some bugs and and improved GenPlay performance. Check out the [[Release_Notes#GenPlay_v996|change log]] for more information.

'''10-15-2013 - ''' [[Release_Notes#GenPlay_v978|GenPlay v978]] released. We corrected some bugs on gene layer operations. Check out the [[Release_Notes#GenPlay_v978|change log]] for more information.

'''09-24-2013 - ''' [[Release_Notes#GenPlay_v976|GenPlay v976]] released! Multiple bugs on the Multi-Genome module have been corrected! Check out the [[Release_Notes#GenPlay_v976|change log]] for more information.

'''08-09-2013 - ''' After almost a year of development, a new revamped version of GenPlay is online! Tracks can now display multiple layers of genome wide data or annotations. The core of the software was completely updated and the data now takes up 2 to 5 times less memory. Loading files is also faster and SAM/BAM files are now supported. Check out the new version (v970). Please help us improve GenPlay by submitting [[Bugs|bugs]] and sending us [mailto:julien.lajugie@einstein.yu.edu?Subject=GenPlay%20Feedback feedback]. Check the [[Release_Notes#GenPlay_v970|change log]] section of the website for more information about the latest version of GenPlay.

'''08-06-2012 - ''' Update of the tutorial [[How to launch a GenPlay jar file]] with a new section: [[How to launch a GenPlay jar file#Launching GenPlay|Launching GenPlay with a file]].

Update of the [[FAQ]]: [[FAQ#I have a Java error when I launch GenPlay, what do I do?|I have a Java error when I launch GenPlay, what do I do?]]

'''05-17-2012 - ''' New GenPlay WebStart launcher! You can now use the Java Web Start Technology to launch any version of GenPlay!! You can also define the amount of memory you want!

'''05-17-2012 - ''' [[Release_Notes#GenPlay_v584|GenPlay release v584]]! Includes a lot of improvements, many changes and fixes a lot of bugs! Check out the [[Release_Notes#GenPlay_v584|change log]] for more information.

'''05-14-2012 - ''' New tutorial: [[How to launch a GenPlay jar file]].

'''05-11-2012 - ''' New Versions page. The previous "Old Versions" page has been replaced by a a new Versions page. It contains the GenPlay change log for a better user experience!

'''03-29-2012 - ''' [[GenPlay Multi-Genome]]. File loader has been improved. GenPlay can now load files with defective lines, which are ignored and reported in a log file.

'''01-30-2012 - ''' [[GenPlay Multi-Genome]]. Many bugs have been fixed. Version is much more stable. Great to visualize results of 1,000 genome projects or your own data.

'''09-13-2011 - ''' [[GenPlay Multi-Genome]] has been incorporated to the standard version of the software. Be aware that the multi-genome functionalities are still under development and might not be totally stable.

'''06-21-2011 -''' The jar file for GenPlay-MG did not work on some platform. The bugs have been fixed. GenPlay-Gg should now run on all platforms. We have also improved the tutorial.

'''06-16-2011 -''' GenPlay Multi-Genome beta is online. Load in Genplay at the same time files mapped in Hg18 and Hg19 ! Compare directly in GenPlay the genomes recently made available by the 1,000 genomes project!. The beta version is now available. Try it and help us make it better by reporting bugs.

'''06-08-2011 -''' Score Repartition Around Start. Look at your data longitudinally ! Version 353 includes promoter pile-up function. Useful to look at average histone modification levels or transcription factor occupancy around transcription start site. Function is quite powerful when combined with the new gene filters.

'''05-26-2011 -''' Filters for gene tracks added. Score exon function now works with variable window tracks.

'''05-23-2011 -''' GenPlay is now published in [http://bioinformatics.oxfordjournals.org/content/early/2011/05/19/bioinformatics.btr309.abstract?ijkey=Rs03fezWf5QYStk&keytype=ref Bioinformatics]. Please [[About GenPlay#Cite GenPlay|quote us ]] to support further developments!

About GenPlay

2016-12-23T18:47:44Z

Julien:

__FORCETOC__

== Introduction ==
GenPlay is an analyzer and browser for high-throughput data that is being developed by the Stem Cell Genomic Unit at the [http://genplay.net/home/default.asp Albert Einstein College of Medicine] of [http://www.yu.edu/ Yeshiva University] in New York City.

== Abstract ==
Rapidly decreasing sequencing cost due to the emergence and improvement of massively-parallel sequencing technologies has resulted in dramatic increase in the quantity of data that need to be analyzed. Therefore, software tools to process, visualize, analyze and integrate data produced on multiple platforms and using multiple methods are needed.

GenPlay is an extremely fast, easy to use and stable tool for rapid analysis and data processing that is being developed at Albert Einstein College of Medicine. Genplay, which is written in Java and runs on all major operating systems, can display data obtained either with micro-array based or sequencing based platforms. It displays tracks adapted to summarize gene structure, gene expression; repeat families, CPG islands, etc. and can also display custom tracks to show the results of RNA-seq, Chip-Seq or TimEX-seq analysis, for example.

GenPlay also offers a library of operations to process raw data (normalization, binning, smoothing) and to generate statistics (minimum, maximum, standard deviation, correlation etc). The tools provided include Gaussian filter, peak finders, signal saturation, island finders. It also has graphical features like scatter plots and bar charts to depict repartition and distances between genes.

The browser is currently being tested and used for in-house studies. The library of operations is growing based on the emerging needs. Contributions to the development of the software are welcome.

== Source Code ==
The source code of GenPlay are available from the GIT repository at https://github.com/JulienLajugie/GenPlay
You can check out the latest source code with a git client with the following command:
git clone git://github.com/JulienLajugie/GenPlay.git

== Report Bugs ==
Please help us improve GenPlay by reporting bugs at https://github.com/JulienLajugie/GenPlay/issues

== Cite GenPlay ==
If you like GenPlay and use it for your research, please help us by citing our publication in [http://bioinformatics.oxfordjournals.org/content/27/14/1889 Bioinformatics]:

Bioinformatics. 2011 May 19
GenPlay, a multi-purpose genome analyzer and browser.
Lajugie J, Bouhassira E.
Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

PMID: 21596789

You can also link to genplay.net from your website to increase our visibility.

Thank you for your support!

== Credit ==
GenPlay is being developed by [mailto:julien.lajugie@gmail.com?Subject=Email%20from%20genplay.net Julien Lajugie], Nicolas Fourel and Eric Bouhassira.
<br>GenPlay was funded in part by [http://stemcell.ny.gov/ NYSTEM]

== License ==
GenPlay, Einstein Genome Analyzer
Copyright (C) 2009, 2013 Albert Einstein College of Medicine

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

The program "GenPlay" written by
[mailto:julien.lajugie@gmail.com?Subject=Email%20from%20genplay.net Julien Lajugie] is available at http://genplay.net

About GenPlay

2016-12-23T18:46:42Z

Julien:

__FORCETOC__

== Introduction ==
GenPlay is an analyzer and browser for high-throughput data that is being developed by the Stem Cell Genomic Unit at the [http://genplay.net/home/default.asp Albert Einstein College of Medicine] of [http://www.yu.edu/ Yeshiva University] in New York City.

== Abstract ==
Rapidly decreasing sequencing cost due to the emergence and improvement of massively-parallel sequencing technologies has resulted in dramatic increase in the quantity of data that need to be analyzed. Therefore, software tools to process, visualize, analyze and integrate data produced on multiple platforms and using multiple methods are needed.

GenPlay is an extremely fast, easy to use and stable tool for rapid analysis and data processing that is being developed at Albert Einstein College of Medicine. Genplay, which is written in Java and runs on all major operating systems, can display data obtained either with micro-array based or sequencing based platforms. It displays tracks adapted to summarize gene structure, gene expression; repeat families, CPG islands, etc. and can also display custom tracks to show the results of RNA-seq, Chip-Seq or TimEX-seq analysis, for example.

GenPlay also offers a library of operations to process raw data (normalization, binning, smoothing) and to generate statistics (minimum, maximum, standard deviation, correlation etc). The tools provided include Gaussian filter, peak finders, signal saturation, island finders. It also has graphical features like scatter plots and bar charts to depict repartition and distances between genes.

The browser is currently being tested and used for in-house studies. The library of operations is growing based on the emerging needs. Contributions to the development of the software are welcome.

== Source Code ==
The source code of GenPlay are available from the GIT repository at https://github.com/JulienLajugie/GenPlay
You can check out the latest source code with a git client with the following command:
git clone git://github.com/JulienLajugie/GenPlay.git

== Report Bugs ==
Please help us improve GenPlay by reporting bugs at https://github.com/JulienLajugie/GenPlay/issues

== Cite GenPlay ==
If you like GenPlay and use it for your research, please help us by citing our publication in [http://bioinformatics.oxfordjournals.org/content/27/14/1889 Bioinformatics]:

Bioinformatics. 2011 May 19
GenPlay, a multi-purpose genome analyzer and browser.
Lajugie J, Bouhassira E.
Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

PMID: 21596789

You can also link to genplay.net from your website to increase our visibility.

Thank you for your support!

== Credit ==
GenPlay is being developed by [mailto:julien.lajugie@gmail.com?Subject=Email%20about%20GenPlay Julien Lajugie], Nicolas Fourel and Eric Bouhassira.
<br>GenPlay was funded in part by [http://stemcell.ny.gov/ NYSTEM]

== License ==
GenPlay, Einstein Genome Analyzer
Copyright (C) 2009, 2013 Albert Einstein College of Medicine

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

The program "GenPlay" written by
[mailto:julien.lajugie@gmail.com?Subject=Email%20about%20GenPlay Julien Lajugie] is available at http://genplay.net

About GenPlay

2016-12-23T18:43:07Z

Julien:

__FORCETOC__

== Introduction ==
GenPlay is an analyzer and browser for high-throughput data that is being developed by the Stem Cell Genomic Unit at the [http://genplay.net/home/default.asp Albert Einstein College of Medicine] of [http://www.yu.edu/ Yeshiva University] in New York City.

== Abstract ==
Rapidly decreasing sequencing cost due to the emergence and improvement of massively-parallel sequencing technologies has resulted in dramatic increase in the quantity of data that need to be analyzed. Therefore, software tools to process, visualize, analyze and integrate data produced on multiple platforms and using multiple methods are needed.

GenPlay is an extremely fast, easy to use and stable tool for rapid analysis and data processing that is being developed at Albert Einstein College of Medicine. Genplay, which is written in Java and runs on all major operating systems, can display data obtained either with micro-array based or sequencing based platforms. It displays tracks adapted to summarize gene structure, gene expression; repeat families, CPG islands, etc. and can also display custom tracks to show the results of RNA-seq, Chip-Seq or TimEX-seq analysis, for example.

GenPlay also offers a library of operations to process raw data (normalization, binning, smoothing) and to generate statistics (minimum, maximum, standard deviation, correlation etc). The tools provided include Gaussian filter, peak finders, signal saturation, island finders. It also has graphical features like scatter plots and bar charts to depict repartition and distances between genes.

The browser is currently being tested and used for in-house studies. The library of operations is growing based on the emerging needs. Contributions to the development of the software are welcome.

== Source Code ==
The source code of GenPlay are available from the GIT repository at https://github.com/JulienLajugie/GenPlay
You can check out the latest source code with a git client with the following command:
git clone git://github.com/JulienLajugie/GenPlay.git

== Report Bugs ==
Please help us improve GenPlay by reporting bugs at https://github.com/JulienLajugie/GenPlay/issues

== Cite GenPlay ==
If you like GenPlay and use it for your research, please help us by citing our publication in [http://bioinformatics.oxfordjournals.org/content/27/14/1889 Bioinformatics]:

Bioinformatics. 2011 May 19
GenPlay, a multi-purpose genome analyzer and browser.
Lajugie J, Bouhassira E.
Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

PMID: 21596789

You can also link to genplay.einstein.yu.edu from your website to increase our visibility.

Thank you for your support!

== Credit ==
GenPlay is being developed by [mailto:julien.lajugie@einstein.yu.edu?Subject=Email%20sent%20from%20genplay.einstein.yu.edu Julien Lajugie], Nicolas Fourel and Eric Bouhassira.
<br>GenPlay was funded in part by [http://stemcell.ny.gov/ NYSTEM]

== License ==
GenPlay, Einstein Genome Analyzer
Copyright (C) 2009, 2013 Albert Einstein College of Medicine

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

The program "GenPlay" written by
[mailto:julien.lajugie@einstein.yu.edu?Subject=Email%20sent%20from%20genplay.einstein.yu.edu Julien Lajugie] is available at http://genplay.einstein.yu.edu

Projects

2016-12-22T21:46:08Z

Julien:

This page contains GenPlay projects available for download. These projects illustrate the type of data analysis and visualization that can be done with GenPlay.
There are two sections: the first one contains projects that were used as supporting data of published articles. The second section contains the projects created for the [[Tutorials]] page of this website.

== How to start a project ==
You first need to download and install GenPlay from the [[Downloads]] page.
Then, you need to download the project you want to launch. Once the download is finished, double click on the project file to start GenPlay and load the project. Loading a project might take a few minutes.

== Projects from published work ==
=== GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface ===
====Authors====
Julien Lajugie, Nicolas Fourel and Eric E Bouhassira
====Abstract====
The number of human genomes sequenced is growing exponentially. The vast majority of these genomes are assembled by comparison to a single reference sequence. This is problematic because of the large amount of genetic variations in human populations. Parallel analysis and visualization of the indels and structural variants present in multiple human genomes is complex because it requires the display of sequences that are unique to specific genomes and absent from the reference sequence. We describe here, GenPlay Multi-Genome, an application that can be used to visualize SNPs, indels and structural variants in multiple human genomes. GenPlay Multi-Genome is ideal for the comparison in a graphic interface of expression and epigenetic data obtained from multiple phased genomes. GenPlay Multi- Genome is also useful to analyze data that has been aligned to custom genomes rather than to a reference genome.
====Article====
[http://bioinformatics.oxfordjournals.org/content/31/1/109.long http://bioinformatics.oxfordjournals.org/content/31/1/109.long]

====GenPlay Project====
[http://genplay.net/library/projects/GenPlay_MG_2014/MG_Demo.zip MG_Demo.zip]

'''Note:''' Uncompress the zip file and double click on MG_demo.gppf to start GenPlay (make sure that GenPlay is installed on your system).

----

=== Allele-Specific Genome-Wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization ===
====Authors====
Rituparna Mukhopadhyay, Julien Lajugie, Nicolas Fourel, Ari Selzer, Michael Schizas, Boris Bartholdy, Jessica Mar, Chii Mei Lin, Melvenia M. Martin, Michael Ryan, Mirit I. Aladjem and Eric E. Bouhassira
====Abstract====
We have developed a new approach based on TimEX-seq to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts. We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated with asynchronously replications. We identified about 600 megabase-sized asynchronously replicated domains in two tested individuals. We show that the longest asynchronously replicated domains are enriched in imprinted genes suggesting that structural variants and parental imprinting are two causes of replication asynchrony in the human genome. Biased chromosome X inactivation in one of the two individuals tested was another source of detectable replication asynchrony. Analysis of high-resolution TimEX profiles revealed timing wrinkles, which are previously undetected, highly reproducible, variations of the timing of replication in the 100kb-range that exist within the well-characterized megabase-sized replication timing domains. We show that these wrinkles correspond to clusters of origins of replication that we detected using novel nascent strands DNA profiling methods. Analysis of the distribution of replication origins revealed dramatic differences in initiation of replication frequency during S phase and a strong association, in both synchronous and asynchronous regions, between origins of replication and three genomic features: G-quadruplexes, CpG Islands and transcription start sites. The frequency of initiation in asynchronous regions was similar in the two homologs. Asynchronous regions were richer in origins of replication than synchronous regions.
====Article====
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004319 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004319]

====GenPlay Project====
[http://genplay.net/library/projects/TimEX-NascentStrands-2013/Timing_and_NS_Profiles_2013.gppf Timing_and_NS_Profiles_2013.gppf]

[http://genplay.net/library/projects/TimEX-NascentStrands-2013/Readme.txt Readme.txt]

----

=== Allele-Specific Analysis of DNA Replication Origins in Mammalian Cells===
====Authors====
Bartholdy B, Mukhopadhyay R, Lajugie J, Aladjem MI, Bouhassira EE
====Abstract====
The mechanisms that control the location and timing of firing of replication origins are poorly understood. Using a novel functional genomic approach based on the analysis of SNPs and indels in phased human genomes, we observe that replication asynchrony is associated with small cumulative variations in the initiation efficiency of multiple origins between the chromosome homologues, rather than with the activation of dormant origins. Allele-specific measurements demonstrate that the presence of G-quadruplex-forming sequences does not correlate with the efficiency of initiation. Sequence analysis reveals that the origins are highly enriched in sequences with profoundly asymmetric G/C and A/T nucleotide distributions and are almost completely depleted of antiparallel triplex-forming sequences. We therefore propose that although G4-forming sequences are abundant in replication origins, an asymmetry in nucleotide distribution, which increases the propensity of origins to unwind and adopt non-B DNA structure, rather than the ability to form G4, is directly associated with origin activity.

====Article====
[http://www.ncbi.nlm.nih.gov/pubmed/25987481 PubMed]

====GenPlay Project====

[http://genplay.net/library/projects/Allele_Specific_NS_Sequencing_FNY01_2_2/AS_Analysis_of_replication_origins.gppf AS_Analysis_of_replication_origins.gppf]

[http://genplay.net/library/projects/Allele_Specific_NS_Sequencing_FNY01_2_2/readme_for_FNY01_2_2_AS_analysis_of_replication_origin_gppf.txt Readme.txt]

----

=== Identification of a BET Family Bromodomain/Casein Kinase II/TAF-Containing Complex as a Regulator of Mitotic Condensin Function ===
====Authors====
Hyun-Soo Kim, Rituparna Mukhopadhyay, Scott B. Rothbart, Andrea C. Silva, Vincent Vanoosthuyse, Ernest Radovani, Thomas Kislinger, Assen Roguev, Colm J. Ryan, Jiewei Xu, Harlizawati Jahari, Kevin G. Hardwick, Jack F. Greenblatt, Nevan J. Krogan, Jeffrey S. Fillingham, Brian D. Strahl, Eric E. Bouhassira, Winfried Edelmann, Michael-Christopher Keogh
====Abstract====
Condensin is a central regulator of mitotic genome structure with mutants showing poorly condensed chromosomes and profound segregation defects. Here, we identify NCT, a complex comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), casein kinase II (CKII), and several TAFs, as a regulator of condensin function. We show that NCT and condensin bind similar genomic regions but only briefly colocalize during the periods of chromosome condensation and decondensation. This pattern of NCT binding at the core centromere, the region of maximal condensin enrichment, tracks the abundance of acetylated histone H4, as regulated by the Hat1-Mis16 acetyltransferase complex and recognized by the first Nrc1 bromodomain. Strikingly, mutants in NCT or Hat1-Mis16 restore the formation of segregation-competent chromosomes in cells containing defective condensin. These results are consistent with a model where NCT targets CKII to chromatin in a cell-cycle-directed manner in order to modulate the activity of condensin during chromosome condensation and decondensation.
====Article====
[http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00063-1 http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00063-1]
====GenPlay Project====
[http://genplay.net/library/projects/CellReports-2014/Kim_CellRep_2014.gppf Kim_CellRep_2014.gppf]

[http://genplay.net/library/projects/CellReports-2014/Readme.txt Readme.txt]

----

=== Methylation ===
Submitted for publication
====Authors====
Boris Bartholdy, Julien Lajugie, Rituparna Mukhopadhyay, John M Greally, Masako Suzuki and Eric E Bouhassira

====Abstract====
Submitted for publication
====Article====
Submitted for publication
====GenPlay Project====

[http://genplay.net/library/projects/Methylation_2016/Methyl_seq_paper_figure_1.gppf Methyl_seq_paper_figure_1.gppf]

[http://genplay.net/library/projects/Methylation_2016/3_2_3_3_AS_methylation_data.gppf 3_2_3_3_AS_methylation_data.gppf]

== Projects from tutorials ==
===ChIP-Seq Tutorial===
====Goal====
The objective of the ChIP-Seq tutorial is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment. Then, to generate a list of genes that have a peak in their promoter and finally to associate the score of the peak summit with each promoter.
====Tutorial====
[[ChIP-Seq Tutorial]]

====Project File====
[http://genplay.net/library/tutorials/ChIP-Seq/ChIP-Seq_Tutorial.gppf ChIP-Seq_Tutorial.gppf]

----

=== TimEX Tutorial===
====Goal====
The TimEX tutorial illustrates how GenPlay can be used to show timing of replication profiles. The goal of the tutorial is to compute the correlation coefficient between the replication timing in human embryonic stem (ES) cells and in primary basophilic erythroblasts derived in culture from primary CD34 positive cells.
====Tutorial====
[[TimEX Tutorial]]
====Project File====
[http://genplay.net/library/tutorials/TimEX/TimEX_Tutorial.gppf TimEX_Tutorial.gppf]

----

=== Multi-Genome Tutorial===

====Goal====
The multi-genome tutorial explains how to display data mapped on genome assembly GRCh37/Hg19 and GRCh38/Hg38 simultaneously.

====Tutorial====
[[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]]

'''Note:''' An older version of this tutorial is available for NCBI36/hg18 - GRCh37/hg19: [[Multi-Genome Tutorial]]

====Project File====
[http://genplay.net/library/tutorials//MG-hg38-hg19/hg19-hg38_Multi-genome.zip hg19-hg38_Multi-genome.zip]

'''Note:''' To start the project you need to unpack the zip archive and to double click on the file called ''hg19-hg38_Multi-genome.gppf''. Make sure that GenPlay is installed on your computer.

'''Note2:''' For the NCBI36/hg18 - GRCh37/hg19 version, click on the following link: [http://genplay.net/library/tutorials/MG-Reference_Genome_Tutorial/GenPlayMG-Reference_Genome_Tutorial.zip GenPlayMG-Reference_Genome_Tutorial.zip]. To start the project you need to unpack the zip archive and to double click on the file called ''GenPlay-MG – Reference genome tutorial.gppf''. Make sure that GenPlay is installed on your computer.

How to Create a VCF File From a Chain File

2014-08-22T15:53:25Z

Julien: /* Creation of chain files */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

'''Note:''' ChainToVCF is an open source program. The source code is available at https://github.com/JulienLajugie/ChainToVCF/

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once this is done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted. Let's call the file hg19ToHg39-SNP.bgr

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===
Put the file generated in the previous chapter into the same directory as ChainToVCF and the chain file.

From there open a terminal, and run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.AddSNPsToVCF--chain ./hg19ToHg38.chain --source hg19 --target hg38 --bgr ./hg19ToHg39-SNP.bgr > hg19ToHg38_complete.vcf

Modify the paths to ChainToVCF.jar, hg19ToHg38.chain and hg19ToHg39-SNP.bgr if needed.

The result VCF file should contain all the differences between hg38 and hg19. You can try to load it into GenPlay.

== Creation of chain files ==

Chains files are described in the following article: http://www.pnas.org/content/100/20/11484.full

A detailed description on how to create chain files can be found at:

* http://genomewiki.ucsc.edu/index.php/LiftOver_Howto
* http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
* http://genomewiki.ucsc.edu/index.php/Chains_Nets

A link to the source code is available at:

* http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/userApps/README

How to Create a VCF File From a Chain File

2014-08-22T15:27:06Z

Julien: /* Creation of chain files */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

'''Note:''' ChainToVCF is an open source program. The source code is available at https://github.com/JulienLajugie/ChainToVCF/

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once this is done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted. Let's call the file hg19ToHg39-SNP.bgr

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===
Put the file generated in the previous chapter into the same directory as ChainToVCF and the chain file.

From there open a terminal, and run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.AddSNPsToVCF--chain ./hg19ToHg38.chain --source hg19 --target hg38 --bgr ./hg19ToHg39-SNP.bgr > hg19ToHg38_complete.vcf

Modify the paths to ChainToVCF.jar, hg19ToHg38.chain and hg19ToHg39-SNP.bgr if needed.

The result VCF file should contain all the differences between hg38 and hg19. You can try to load it into GenPlay.

== Creation of chain files ==

Chains files are described in the following article: http://www.pnas.org/content/100/20/11484.full

A detailed description on how to create chain files can be found at:

* http://genomewiki.ucsc.edu/index.php/LiftOver_Howto
* http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
* http://genomewiki.ucsc.edu/index.php/Chains_Nets

The source code for is available at:

* http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/userApps/README

How to Create a VCF File From a Chain File

2014-08-22T15:25:24Z

Julien: /* Generate a VCF with the Insertions and the Deletions */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

'''Note:''' ChainToVCF is an open source program. The source code is available at https://github.com/JulienLajugie/ChainToVCF/

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once this is done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted. Let's call the file hg19ToHg39-SNP.bgr

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===
Put the file generated in the previous chapter into the same directory as ChainToVCF and the chain file.

From there open a terminal, and run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.AddSNPsToVCF--chain ./hg19ToHg38.chain --source hg19 --target hg38 --bgr ./hg19ToHg39-SNP.bgr > hg19ToHg38_complete.vcf

Modify the paths to ChainToVCF.jar, hg19ToHg38.chain and hg19ToHg39-SNP.bgr if needed.

The result VCF file should contain all the differences between hg38 and hg19. You can try to load it into GenPlay.

== Creation of chain files ==

Chains files are described in : http://www.pnas.org/content/100/20/11484.full

A detailed description on how to create chain file can be found at:

* http://genomewiki.ucsc.edu/index.php/LiftOver_Howto
* http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
* http://genomewiki.ucsc.edu/index.php/Chains_Nets

The source code for is available at:

* http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/userApps/README

How to Create a VCF File From a Chain File

2014-08-22T15:23:54Z

Julien:

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

'note:' ChainToVCF is an open source program. The code source is available at https://github.com/JulienLajugie/ChainToVCF/

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once this is done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted. Let's call the file hg19ToHg39-SNP.bgr

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===
Put the file generated in the previous chapter into the same directory as ChainToVCF and the chain file.

From there open a terminal, and run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.AddSNPsToVCF--chain ./hg19ToHg38.chain --source hg19 --target hg38 --bgr ./hg19ToHg39-SNP.bgr > hg19ToHg38_complete.vcf

Modify the paths to ChainToVCF.jar, hg19ToHg38.chain and hg19ToHg39-SNP.bgr if needed.

The result VCF file should contain all the differences between hg38 and hg19. You can try to load it into GenPlay.

== Creation of chain files ==

Chains files are described in : http://www.pnas.org/content/100/20/11484.full

A detailed description on how to create chain file can be found at:

* http://genomewiki.ucsc.edu/index.php/LiftOver_Howto
* http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
* http://genomewiki.ucsc.edu/index.php/Chains_Nets

The source code for is available at:

* http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/userApps/README

Tutorials

2014-08-22T15:18:54Z

Julien: /* How to Create a VCF File From a Chain File */

The following tutorials aim to give you some of the basic concept on the track manipulation techniques.

== ChIP-Seq Analysis ==
The objective of the [[ChIP-Seq Tutorial]] is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment.

== TimEX Analysis ==
The [[TimEX Tutorial]] illustrates how GenPlay can be used to show timing of replication profiles.

== Multi-Genome Analysis ==
The [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] explains how to use the multi-genome functionality of GenPlay.

It shows how data aligned on hg38 and hg19 can be displayed simultaneously and compared using GenPlay Multi-Genome

'''Note:''' Here is a version for the comparison of hg18 and hg19: [[Multi-Genome Tutorial]].

== How to Create a VCF File From a Chain File ==
The goal of [[How to Create a VCF File From a Chain File|this tutorial]] is to show how to generate a VCF file such as the one used in the [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] from a Chain file that can be downloaded from the UCSC genome browser website.

How to Create a VCF File From a Chain File

2014-08-11T05:19:02Z

Julien: /* Adding the SNPs to the VCF File */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once this is done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted. Let's call the file hg19ToHg39-SNP.bgr

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===
Put the file generated in the previous chapter into the same directory as ChainToVCF and the chain file.

From there open a terminal, and run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.AddSNPsToVCF--chain ./hg19ToHg38.chain --source hg19 --target hg38 --bgr ./hg19ToHg39-SNP.bgr > hg19ToHg38_complete.vcf

Modify the paths to ChainToVCF.jar, hg19ToHg38.chain and hg19ToHg39-SNP.bgr if needed.

The result VCF file should contain all the differences between hg38 and hg19. You can try to load it into GenPlay.

How to Create a VCF File From a Chain File

2014-08-11T05:18:02Z

Julien: /* Adding the SNPs to the VCF File */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once this is done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted. Let's call the file hg19ToHg39-SNP.bgr

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===
Put the file generated in the previous chapter into the same directory as ChainToVCF and the chain file.

From there open a terminal, and run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.AddSNPsToVCF--chain ./hg19ToHg38.chain --source hg19 --target hg38 --bgr ./ > hg19ToHg38_complete.vcf

Modify the paths to ChainToVCF.jar, hg19ToHg38.chain and if needed.

The result VCF file should contain all the differences between hg38 and hg19.

How to Create a VCF File From a Chain File

2014-08-11T05:14:12Z

Julien: /* Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once this is done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted. Let's call the file hg19ToHg39-SNP.bgr

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===

How to Create a VCF File From a Chain File

2014-08-11T05:13:17Z

Julien: /* Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once this is done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted.

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===

How to Create a VCF File From a Chain File

2014-08-11T05:12:45Z

Julien: /* Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once it's done, right click on the track handler of the newly created layer, select the layer sub-menu at the bottom of the contextual menu and select "Save As" (figure 2). Select a BGR extension in the file dialog and select hg38 as the reference genome when prompted.

[[image: ChainToVCFTutorial_Figure2.png|center|frame|Figure 2: Save layer]]

=== Adding the SNPs to the VCF File ===

File:ChainToVCFTutorial Figure2.png

2014-08-11T05:12:35Z

Julien:

File:ChainToVCFTutorial Figure1.png

2014-08-11T05:07:42Z

Julien: uploaded a new version of "File:ChainToVCFTutorial Figure1.png"

File:ChainToVCFTutorial Figure1.png

2014-08-11T05:06:33Z

Julien:

How to Create a VCF File From a Chain File

2014-08-11T05:06:10Z

Julien: /* Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay */

'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg19 to hg38 VCF file. This means that the reference genome of the VCF file is hg38.

The tutorial is divided into two steps. The first step consists in generating a VCF containing the insertions and the deletions using a Chain file and a program developed in Scala called ChainToVCF.

In the second step we will use GenPlay and ChainToVCF to add SNPs to our VCF file.

'''Prerequisite:'''
You will need to have a '''Linux''' or '''Mac''' computer.

'''Scala''' needs to be installed on you computer. Scala is available to download from http://www.scala-lang.org/download/

'''GenPlay''' needs to be installed on your computer. If you haven't installed GenPlay yet, please visit the [[Downloads]] page and follow the instructions to download and install GenPlay.

== Getting started ==
First, let's download the files needed from the UCSC genome browser. All the file are available from [http://hgdownload.cse.ucsc.edu/downloads.html#human the download page] of the UCSC genome browser. We will need the following:

1. hg19 to hg38 chain file (this file can be found in the LiftOver section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

2. hg19 reference file in 2bit format (from the full dataset section): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

3. h38 reference file in 2bit format: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Note that the chain file needs to be uncompressed.

== Generate a VCF with the Insertions and the Deletions ==
In order to generate our VCF file we will need the Scala program ChainToVCF available at https://github.com/JulienLajugie/ChainToVCF/releases/download/V1.0/ChainToVCF.jar

First, make sure that Scala is properly installed on your system.

Then, from a terminal, run the following command:

scala -classpath ./ChainToVCF.jar edu.yu.einstein.chainToVCF.ChainToVCF --chain ./hg19ToHg38.chain --source hg19 --target hg38 > hg19ToHg38.vcf

Modify the paths to ChainToVCF.jar and hg19ToHg38.chain if needed.

The resulting VCF will contain all the insertion and deletion of hg19 using hg38 as a reference genome. In the next step we will add the SNPs to our VCF file.

== Add SNPs to the VCF File ==
The process of adding SNPs to the VCF file can be divided into two parts.

We will first extract the differences between the hg19 and hg38 sequences. GenPlay can generate a BGR file containing these differences.

After that, we will use use the ChainToVCF program previously downloaded to add SNPs to the VCF file.

=== Generate a BGR File Containing the Remaining Differences Between hg19 and hg38 Using GenPlay ===

To add SNPs to the VCF file we need to extract the remaining differences from the sequences of hg19 and hg38. This can be done using GenPlay.

You first need to go through the following tutorial [[hg19_GRCh38/hg38_Multi-Genome_Tutorial]]. Use the VCF generated during the previous phase instead of the one provided for the tutorial.

At the end of the tutorial you should end up with a sequence layer for hg19 and a sequence layer for hg38. Right click on the track handler of the hg38 track handler and select the hg38 layer at the bottom of the contextual menu and then select the Compare Sequences option (figure 1). Select hg19 when prompter to select a second layer and select an empty track for the result.

[[image: ChainToVCFTutorial_Figure1.png|center|frame|Figure 1: Compare Sequences]]
Generating the differences between two sequence layer is slow and can take a couple hour.

Once it's done, right click on the track handler where the

=== Adding the SNPs to the VCF File ===

How to Create a VCF File From a Chain File

2014-08-11T05:03:43Z

Julien: /* Add SNPs to the VCF File */

How to Create a VCF File From a Chain File

2014-08-11T05:02:59Z

Julien:

How to Create a VCF File From a Chain File

2014-08-11T05:02:05Z

Julien: /* Generate a VCF with the Insertions and the Deletions */

How to Create a VCF File From a Chain File

2014-08-11T05:00:57Z

Julien: /* Add SNPs to the VCF File */

How to Create a VCF File From a Chain File

2014-08-11T04:47:26Z

Julien: /* Generate a VCF with the Insertions and the Deletions */

How to Create a VCF File From a Chain File

2014-08-11T04:47:04Z

Julien: /* Add SNPs to the VCF File */

How to Create a VCF File From a Chain File

2014-08-11T04:37:57Z

Julien:

How to Create a VCF File From a Chain File

2014-08-10T22:09:36Z

Julien: /* Generate a VCF with the Insertions and the Deletions */

How to Create a VCF File From a Chain File

2014-08-10T19:58:50Z

Julien: /* Generate a VCF with the Insertions and the Deletions */

How to Create a VCF File From a Chain File

2014-08-10T19:57:56Z

Julien:

How to Create a VCF File From a Chain File

2014-08-10T19:57:44Z

Julien: /* Generate a VCF with the Insertions and the Deletions */

How to Create a VCF File From a Chain File

2014-08-10T19:57:30Z

Julien: /* Generate a VCF with the Insertions and the Deletions */

How to Create a VCF File From a Chain File

2014-08-10T19:56:55Z

Julien: /* Getting started */

How to Create a VCF File From a Chain File

2014-08-10T19:56:30Z

Julien: /* Generate a VCF with the Insertions and the Deletions */

How to Create a VCF File From a Chain File

2014-08-10T19:55:29Z

Julien: /* Generate a VCF with the insertion and the deletion */

How to Create a VCF File From a Chain File

2014-08-10T19:49:55Z

Julien:

How to Create a VCF File From a Chain File

2014-08-10T19:48:53Z

Julien:

How to Create a VCF File From a Chain File

2014-08-10T19:48:14Z

Julien:

How to Create a VCF File From a Chain File

2014-08-10T19:47:31Z

Julien:

How to Create a VCF File From a Chain File

2014-08-10T19:47:21Z

Julien: /* Getting started */

How to Create a VCF File From a Chain File

2014-08-10T19:41:44Z

Julien: /* Getting started */

How to Create a VCF File From a Chain File

2014-08-10T19:41:31Z

Julien: Created page with "'''Goal''': This tutorial illustrates how to generate a VCF file describing the differences between two reference genomes from a Chain file. In this tutorial we will create a hg1..."

Tutorials

2014-08-10T19:27:58Z

Julien: /* How to Create a VCF File From a Chain file */

The following tutorials aim to give you some of the basic concept on the track manipulation techniques.

== ChIP-Seq Analysis ==
The objective of the [[ChIP-Seq Tutorial]] is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment.

== TimEX Analysis ==
The [[TimEX Tutorial]] illustrates how GenPlay can be used to show timing of replication profiles.

== Multi-Genome Analysis ==
The [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] explains how to use the multi-genome functionality of GenPlay.

It shows how data aligned on hg38 and hg19 can be displayed simultaneously and compared using GenPlay Multi-Genome

'''Note:''' Here is a version for the comparison of hg18 and hg19: [[Multi-Genome Tutorial]].

== How to Create a VCF File From a Chain File ==
The goal of this [[How to Create a VCF File From a Chain File|tutorial]] is to show how to generate a VCF file such as the one used in the [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] from a Chain file that can be downloaded from the UCSC genome browser website.

Tutorials

2014-08-10T19:26:38Z

Julien: /* How to Create a VCF File From a Chain file */

The following tutorials aim to give you some of the basic concept on the track manipulation techniques.

== ChIP-Seq Analysis ==
The objective of the [[ChIP-Seq Tutorial]] is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment.

== TimEX Analysis ==
The [[TimEX Tutorial]] illustrates how GenPlay can be used to show timing of replication profiles.

== Multi-Genome Analysis ==
The [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] explains how to use the multi-genome functionality of GenPlay.

It shows how data aligned on hg38 and hg19 can be displayed simultaneously and compared using GenPlay Multi-Genome

'''Note:''' Here is a version for the comparison of hg18 and hg19: [[Multi-Genome Tutorial]].

== How to Create a VCF File From a Chain file ==
The goal of this tutorial is to show how to generate a VCF file such as the one used in the [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] from a Chain file that can be downloaded from the UCSC genome browser website.

Tutorials

2014-08-10T19:26:15Z

Julien:

The following tutorials aim to give you some of the basic concept on the track manipulation techniques.

== ChIP-Seq Analysis ==
The objective of the [[ChIP-Seq Tutorial]] is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment.

== TimEX Analysis ==
The [[TimEX Tutorial]] illustrates how GenPlay can be used to show timing of replication profiles.

== Multi-Genome Analysis ==
The [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] explains how to use the multi-genome functionality of GenPlay.

It shows how data aligned on hg38 and hg19 can be displayed simultaneously and compared using GenPlay Multi-Genome

'''Note:''' Here is a version for the comparison of hg18 and hg19: [[Multi-Genome Tutorial]].

== How to Create a VCF File From a Chain file ==
The goal of this tutorial is to show how to generate a VCF file such as the one used in the [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] from a Chain file that can be downloaded on the UCSC genome browser website.

News

2014-06-30T21:19:30Z

Julien: /* Updates */

== Updates ==
'''06-30-2014 - ''' [[Release_Notes#GenPlay_v1.1.0|GenPlay v1.1.0]] released. The version 1.1.0 is out. GenPlay can now be [[Downloads|installed]] on Windows, Mac and Linux. Project and track files can be double clicked from a file explorer. Tracks can be dragged and dropped between instances of GenPlay, or between GenPlay and an explorer.

'''01-09-2014 - ''' [[Release_Notes#GenPlay_v996|GenPlay v996]] released. We corrected some bugs and and improved GenPlay performance. Check out the [[Release_Notes#GenPlay_v996|change log]] for more information.

'''10-15-2013 - ''' [[Release_Notes#GenPlay_v978|GenPlay v978]] released. We corrected some bugs on gene layer operations. Check out the [[Release_Notes#GenPlay_v978|change log]] for more information.

'''09-24-2013 - ''' [[Release_Notes#GenPlay_v976|GenPlay v976]] released! Multiple bugs on the Multi-Genome module have been corrected! Check out the [[Release_Notes#GenPlay_v976|change log]] for more information.

'''08-09-2013 - ''' After almost a year of development, a new revamped version of GenPlay is online! Tracks can now display multiple layers of genome wide data or annotations. The core of the software was completely updated and the data now takes up 2 to 5 times less memory. Loading files is also faster and SAM/BAM files are now supported. Check out the new version (v970). Please help us improve GenPlay by submitting [[Bugs|bugs]] and sending us [mailto:julien.lajugie@einstein.yu.edu?Subject=GenPlay%20Feedback feedback]. Check the [[Release_Notes#GenPlay_v970|change log]] section of the website for more information about the latest version of GenPlay.

'''08-06-2012 - ''' Update of the tutorial [[How to launch a GenPlay jar file]] with a new section: [[How to launch a GenPlay jar file#Launching GenPlay|Launching GenPlay with a file]].

Update of the [[FAQ]]: [[FAQ#I have a Java error when I launch GenPlay, what do I do?|I have a Java error when I launch GenPlay, what do I do?]]

'''05-17-2012 - ''' New GenPlay WebStart launcher! You can now use the Java Web Start Technology to launch any version of GenPlay!! You can also define the amount of memory you want!

'''05-17-2012 - ''' [[Release_Notes#GenPlay_v584|GenPlay release v584]]! Includes a lot of improvements, many changes and fixes a lot of bugs! Check out the [[Release_Notes#GenPlay_v584|change log]] for more information.

'''05-14-2012 - ''' New tutorial: [[How to launch a GenPlay jar file]].

'''05-11-2012 - ''' New Versions page. The previous "Old Versions" page has been replaced by a a new Versions page. It contains the GenPlay change log for a better user experience!

'''03-29-2012 - ''' [[GenPlay Multi-Genome]]. File loader has been improved. GenPlay can now load files with defective lines, which are ignored and reported in a log file.

'''01-30-2012 - ''' [[GenPlay Multi-Genome]]. Many bugs have been fixed. Version is much more stable. Great to visualize results of 1,000 genome projects or your own data.

'''09-13-2011 - ''' [[GenPlay Multi-Genome]] has been incorporated to the standard version of the software. Be aware that the multi-genome functionalities are still under development and might not be totally stable.

'''06-21-2011 -''' The jar file for GenPlay-MG did not work on some platform. The bugs have been fixed. GenPlay-Gg should now run on all platforms. We have also improved the tutorial.

'''06-16-2011 -''' GenPlay Multi-Genome beta is online. Load in Genplay at the same time files mapped in Hg18 and Hg19 ! Compare directly in GenPlay the genomes recently made available by the 1,000 genomes project!. The beta version is now available. Try it and help us make it better by reporting bugs.

'''06-08-2011 -''' Score Repartition Around Start. Look at your data longitudinally ! Version 353 includes promoter pile-up function. Useful to look at average histone modification levels or transcription factor occupancy around transcription start site. Function is quite powerful when combined with the new gene filters.

'''05-26-2011 -''' Filters for gene tracks added. Score exon function now works with variable window tracks.

'''05-23-2011 -''' GenPlay is now published in [http://bioinformatics.oxfordjournals.org/content/early/2011/05/19/bioinformatics.btr309.abstract?ijkey=Rs03fezWf5QYStk&keytype=ref Bioinformatics]. Please [[About GenPlay#Cite GenPlay|quote us ]] to support further developments!

== In Progress ==
=== GenPlay Multi Genome ===
We are actively working on improving [[GenPlay Multi-Genome|Multi-Genome]] functionalities of GenPlay.

The [[Multi-Genome Tutorial]] explains how to use these functionalities.

News

2014-06-30T21:19:09Z

Julien: /* Updates */

== Updates ==
'''06-30-2014 - ''' [[Release_Notes#GenPlay_v1.1.0|GenPlay v1.1.0]] released. The version 1.1.0 is out. GenPlay can now be [[Downloads|installed]] on Windows, Mac and Linux. Project and track files can be double clicked from a file explorer. Tracks can be dragged and dropped between instances of GenPlay, or between GenPlay and an explorer.

'''01-09-2014 - ''' [[Release_Notes#GenPlay_v996|GenPlay v996]] released. We corrected some bugs and and improved GenPlay performance. Check out the [[Versions#GenPlay_v996|change log]] for more information.

'''10-15-2013 - ''' [[Release_Notes#GenPlay_v978|GenPlay v978]] released. We corrected some bugs on gene layer operations. Check out the [[Versions#GenPlay_v978|change log]] for more information.

'''09-24-2013 - ''' [[Release_Notes#GenPlay_v976|GenPlay v976]] released! Multiple bugs on the Multi-Genome module have been corrected! Check out the [[Versions#GenPlay_v976|change log]] for more information.

'''08-09-2013 - ''' After almost a year of development, a new revamped version of GenPlay is online! Tracks can now display multiple layers of genome wide data or annotations. The core of the software was completely updated and the data now takes up 2 to 5 times less memory. Loading files is also faster and SAM/BAM files are now supported. Check out the new version (v970). Please help us improve GenPlay by submitting [[Bugs|bugs]] and sending us [mailto:julien.lajugie@einstein.yu.edu?Subject=GenPlay%20Feedback feedback]. Check the [[Release_Notes#GenPlay_v970|change log]] section of the website for more information about the latest version of GenPlay.

'''08-06-2012 - ''' Update of the tutorial [[How to launch a GenPlay jar file]] with a new section: [[How to launch a GenPlay jar file#Launching GenPlay|Launching GenPlay with a file]].

Update of the [[FAQ]]: [[FAQ#I have a Java error when I launch GenPlay, what do I do?|I have a Java error when I launch GenPlay, what do I do?]]

'''05-17-2012 - ''' New GenPlay WebStart launcher! You can now use the Java Web Start Technology to launch any version of GenPlay!! You can also define the amount of memory you want!

'''05-17-2012 - ''' [[Release_Notes#GenPlay_v584|GenPlay release v584]]! Includes a lot of improvements, many changes and fixes a lot of bugs! Check out the [[Release_Notes#GenPlay_v584|change log]] for more information.

'''05-14-2012 - ''' New tutorial: [[How to launch a GenPlay jar file]].

'''05-11-2012 - ''' New Versions page. The previous "Old Versions" page has been replaced by a a new Versions page. It contains the GenPlay change log for a better user experience!

'''03-29-2012 - ''' [[GenPlay Multi-Genome]]. File loader has been improved. GenPlay can now load files with defective lines, which are ignored and reported in a log file.

'''01-30-2012 - ''' [[GenPlay Multi-Genome]]. Many bugs have been fixed. Version is much more stable. Great to visualize results of 1,000 genome projects or your own data.

'''09-13-2011 - ''' [[GenPlay Multi-Genome]] has been incorporated to the standard version of the software. Be aware that the multi-genome functionalities are still under development and might not be totally stable.

'''06-21-2011 -''' The jar file for GenPlay-MG did not work on some platform. The bugs have been fixed. GenPlay-Gg should now run on all platforms. We have also improved the tutorial.

'''06-16-2011 -''' GenPlay Multi-Genome beta is online. Load in Genplay at the same time files mapped in Hg18 and Hg19 ! Compare directly in GenPlay the genomes recently made available by the 1,000 genomes project!. The beta version is now available. Try it and help us make it better by reporting bugs.

'''06-08-2011 -''' Score Repartition Around Start. Look at your data longitudinally ! Version 353 includes promoter pile-up function. Useful to look at average histone modification levels or transcription factor occupancy around transcription start site. Function is quite powerful when combined with the new gene filters.

'''05-26-2011 -''' Filters for gene tracks added. Score exon function now works with variable window tracks.

'''05-23-2011 -''' GenPlay is now published in [http://bioinformatics.oxfordjournals.org/content/early/2011/05/19/bioinformatics.btr309.abstract?ijkey=Rs03fezWf5QYStk&keytype=ref Bioinformatics]. Please [[About GenPlay#Cite GenPlay|quote us ]] to support further developments!

== In Progress ==
=== GenPlay Multi Genome ===
We are actively working on improving [[GenPlay Multi-Genome|Multi-Genome]] functionalities of GenPlay.

The [[Multi-Genome Tutorial]] explains how to use these functionalities.