Difference between revisions of "GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial"
From GenPlay, Einstein Genome Analyzer
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'''Note:''' The final result of this tutorial is available as a project that can be loaded from the [[Projects#GRCh37/Hg19 GRCh38/Hg38 Multi-Genome Tutorial| Projects]] page of this website. | '''Note:''' The final result of this tutorial is available as a project that can be loaded from the [[Projects#GRCh37/Hg19 GRCh38/Hg38 Multi-Genome Tutorial| Projects]] page of this website. | ||
| + | |||
| + | == Getting started == | ||
| + | In order to set up and manage a Multi-Genome Project in Genplay, please refer to the following sections of the documentation: | ||
| + | * [[Documentation#Multi Genome Project|Loading a Multi Genome Project]] | ||
| + | * [[Documentation#Loading a Variant Layer|Loading a Variant Layer]] | ||
| + | * [[Documentation#Variant Layer Operations|Variant Layer operations]] | ||
| + | |||
| + | == Downloading Files == | ||
| + | *[http://genplay.einstein.yu.edu/library/tutorials/MG-hg38-hg19/hg19ToHg38_settings.xml XML settings file] | ||
| + | *[http://genplay.einstein.yu.edu/library/tutorials/MG-hg38-hg19/hg19ToHg38.vcf.gz VCF file] | ||
| + | *[http://genplay.einstein.yu.edu/library/tutorials/MG-hg38-hg19/hg19ToHg38.vcf.gz.tbi Indexed VCF file (Tabix)] | ||
| + | *[http://genplay.einstein.yu.edu/library/Human/hg38/Gene_Annotation/Genes_RefSeq_hg38_06.05.2014.bed Refseq BED file for NCBI38/hg38] | ||
| + | *[http://genplay.einstein.yu.edu/library/Human/hg19/Gene_Annotation/Genes_RefSeq_hg19_09.20.2013.bed Refseq BED file for GRCh37/hg19] | ||
| + | |||
| + | == Starting a New Project == | ||
| + | After starting GenPlay you will be prompted to select a name, a clade, a genome and an assembly for your project. | ||
| + | You can enter "hg19 - hg38 Tutorial" for the name, select the mammal clade, the human genome and the hg38 assembly (figure 1). | ||
| + | [[image: hg19-38_tutorial_project_frame.png|center|frame|Figure 1: New Project Window]] | ||
| + | Then, click on the tool box button on the assembly line. A new window will appear allowing you to select chromosomes. For this tutorial we will work only on the basic chromosomes (chr1 to chr22 plus chrX and Y) . You can select the basic chromosomes by clicking on the ''Basics'' (figure 2). | ||
| + | [[image: hg19-38_tutorial_chromo_selection.png|center|frame|Figure 2: Project Chromosomes]] | ||
| + | |||
| + | === Selecting the Reference Assembly === | ||
| + | |||
| + | === Setting the Multi-Genome Parameters === | ||
| + | |||
| + | == Displaying SNPs, Insertions and Deletions == | ||
| + | |||
| + | == Displaying Gene Annotation Layers == | ||
Revision as of 15:19, 25 June 2014
Goal: This tutorial illustrates how the multi-genome mode of GenPlay can be used to simultaneously display data aligned on different reference genome. In this tutorial we will compare gene annotation data aligned on GRCh37/Hg19 with gene annotation data aligned on GRCh38/Hg38.
Prerequisite: GenPlay need to be installed on your computer. If you haven't installed GenPlay yet, please visit the Downloads page and follow the instruction to download and install GenPlay.
Note: The final result of this tutorial is available as a project that can be loaded from the Projects page of this website.
Contents
Getting started
In order to set up and manage a Multi-Genome Project in Genplay, please refer to the following sections of the documentation:
Downloading Files
- XML settings file
- VCF file
- Indexed VCF file (Tabix)
- Refseq BED file for NCBI38/hg38
- Refseq BED file for GRCh37/hg19
Starting a New Project
After starting GenPlay you will be prompted to select a name, a clade, a genome and an assembly for your project. You can enter "hg19 - hg38 Tutorial" for the name, select the mammal clade, the human genome and the hg38 assembly (figure 1).
Then, click on the tool box button on the assembly line. A new window will appear allowing you to select chromosomes. For this tutorial we will work only on the basic chromosomes (chr1 to chr22 plus chrX and Y) . You can select the basic chromosomes by clicking on the Basics (figure 2).
