|
|
| Line 1: |
Line 1: |
| − | == Getting started ==
| + | In order to set up and manage a Multi-Genome Project in Genplay, please refer to the following sections of the documentation: |
| − | === Introduction ===
| + | * [[Documentation#Multi Genome Project|Loading a Multi Genome Project]] |
| − | To create a multi-genome session, users must first load VCF files. VCF files are files that describe all the differences between a reference genome and a particular genome.
| + | * [[Documentation#Loading a Variant Layer|Loading a Variant Layer]] |
| − | | + | * [[Documentation#Variant Layer Operations|Variant Layer operations]] |
| − | The first part of this tutorial presents how to set up a multi-genome project, especially how to load VCF files.
| |
| − | The second part concerns loading data layers onto tracks. Data layers must be mapped to one of the loaded genomes.
| |
| − | Finally, we will describe how to highlight information from VCF files.
| |
| − | | |
| − | === The Welcome screen ===
| |
| − | The welcome screen is the first screen of GenPlay-MG and allow user to create or to load a project.
| |
| − | | |
| − | ==== New Project ====
| |
| − | In order to create a new project, users must give it a name as shown in Figure 1.
| |
| − | [[image:mg_basics_project name.png|center|frame|Figure 1: Text field to define the project name]]
| |
| − | <br/>
| |
| − | The second step is to choose a reference genome. Users can choose it using the different list according to the clade, the genome and the assembly (Figure 2).
| |
| − | [[image:mg_basics_assembly_chooser.png|center|frame|Figure 2: Assembly chooser]]
| |
| − | <br/>
| |
| − | Several chromosomes are available for each assembly but users can choose to select only some of them.<br/>
| |
| − | To open the chromosome chooser (Figure 3), users have to click on the tools button next to the assembly name.
| |
| − | [[image:mg_basics_chromosome_chooser.png|center|frame|Figure 3: Chromosome chooser]] | |
| − | <br/>
| |
| − | The third and last step is to choose between a ''Simple Genome Project'' and a ''Multi Genome Project''. This tutorial is about multi genome project, after having checked this option, the welcome screen should be as the one shown in Figure 4.
| |
| − | [[image:mg_basics_empty_welcome_screen.png|center|frame|Figure 4: Empty welcome screen for multi-genome project]]
| |
| − | <br/>
| |
| − | | |
| − | ==== Load Project ====
| |
| − | Coming soon<br/>
| |
| − | (Option unavailable in the beta version)
| |
| − | | |
| − | === VCF Files ===
| |
| − | ==== Description ====
| |
| − | VCF files describe differences between genomes. Usually, it concerns differences between one or several genomes of interest and the reference genome used for the mapping process. VCF files define multiple type of variations; GenPlay is able to read and represent the followings:
| |
| − | * InDels
| |
| − | * SNPs | |
| − | * SV (Structural Variation)
| |
| − | <br/>
| |
| − | A complete description of VCF files is given on the 1000 genomes project website:<br/>
| |
| − | [http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42 Variant Call Format specification]<br/> | |
| − | | |
| − | ==== Tabix ====
| |
| − | ===== Introduction =====
| |
| − | VCF files contain a lot of information which makes the scanning (loading) processes longer.<br/>
| |
| − | In order to increase the scanning efficiency, VCF files have to be compressed and indexed. The compression is done using BGZip and the indexing with Tabix.<br/>
| |
| − | [http://samtools.sourceforge.net/tabix.shtml Tabix manual reference pages]<br/> | |
| − | [http://sourceforge.net/projects/samtools/files/tabix/ Tabix download]
| |
| − | | |
| − | ===== VCF files indexing methods =====
| |
| − | ====== Using GenPlay ======
| |
| − | GenPlay is now able to compress and index VCF files using the VCF Loader.<br/>
| |
| − | That process is detailed below on the VCF files loading section.<br/>
| |
| − | It is fully automatic and non-platform dependent (works on Windows, Linux and Mac).
| |
| − | ====== Manually ======
| |
| − | First, please note the following process must be performed in either Linux or Mac environments.<br/>
| |
| − | Each VCF files must be first compress to a BGZF (.bgz file) format. Tabix provides a tool to perform the compression.
| |
| − | After compression, VCF files must be indexed using the associated command.
| |
| − | Once Tabix is installed, two commands are necessary to perform the indexation.
| |
| − | <br/><br/>
| |
| − | | |
| − | Available commands from the Tabix folder:<br/>
| |
| − | ''bgzip -f VCF_PATH;''<br/>
| |
| − | ''tabix –p vcf VCF_PATH;''
| |
| − | <br/><br/>
| |
| − | | |
| − | For example, a VCF file named my_vcf.vcf located in the same folder as Tabix can be indexed with the following commands (Figure 5):<br/>
| |
| − | ''bgzip -f ./my_vcf.vcf;''<br/>
| |
| − | ''tabix –p vcf ./my_vcf.vcf.gz;''
| |
| − | [[image:mg_basics_indexation_commands.png|center|frame|Figure 5: VCF file indexation command]]
| |
| − | <br/><br/>
| |
| − | | |
| − | '''Note:''' the first command '''replaces''' the current VCF file by the compressed VCF file (.vcf.gz). The second command '''creates''' the indexed VCF file in the current folder (.vcf.gz.tbi).<br/>
| |
| − | More options are available on [http://samtools.sourceforge.net/tabix.shtml Tabix manual reference pages].
| |
| − | | |
| − | === VCF files loading ===
| |
| − | | |
| − | ==== The VCF Loader ====
| |
| − | ===== Introduction =====
| |
| − | The VCF Loader is the most important part of multi-genome project settings. It allows users to load all necessary VCF files and to define how to extract information from them. It appears when users click on the "Edit" button from the welcome screen.<br/>
| |
| − | The Figure 6 shows an empty VCF Loader screen.
| |
| − | [[image:Mg_welcome_screen_vcf_loader.png|center|frame|Figure 6: VCF loader]] | |
| − | <br/>
| |
| − | | |
| − | GenPlay-MG does not use directly the VCF file, it uses a compress version of it (.gz). Moreover, GenPlay-MG also needs the compress VCF file to be indexed with Tabix. Both file versions must be in the '''same folder''' and must have the '''same name''', only file extensions differ (.gz and .tbi).
| |
| − | | |
| − | By right clicking, the user can add or remove rows.
| |
| − | | |
| − | ===== Columns description =====
| |
| − | '''''File'''''<br/>
| |
| − | This column refers to the VCF file path. Once loaded, the raw name column is automatically filled with every raw genome name contained in the selected VCF file.<br/>
| |
| − | '''''Raw name'''''<br/>
| |
| − | The ''Raw name'' column list is automatically filled when a VCF file has been chosen. That list contains every genotype headers contained inside the selected VCF file. Because Genome names might be difficult to remembers, GenPlay-MG offers users the option of adding another name (an alias) using the ''Genome'' column.<br/>
| |
| − | '''''Nickname'''''<br/>
| |
| − | The ''Nickname'' column allows users to associate an alias to the selected genome. This alias will appear in GenPlay-MG and can be useful because genome names in VCF files are often non descriptive numbers that can be hard to remember.<br/>
| |
| − | '''''Group'''''<br/>
| |
| − | Users can gather genomes by group. Group names are used to distinguish genomes and to perform some specific functionalities.<br/>
| |
| − | | |
| − | ===== Columns edition =====
| |
| − | ''Group'', ''Nickname'' and ''File'' column have their own editable list.To edit a cell, click on it, go over the item you want to edit and choose one of the following action:<br/>
| |
| − | - Add (green symbol on empty item)<br/>
| |
| − | - Edit (pen symbol on an item)<br/>
| |
| − | - Delete (red symbol on an item)<br/>
| |
| − | | |
| − | That way, users can set up all columns before starting (or at the same time) to fill the table.<br/>
| |
| − | | |
| − | '''Note: ''' The ''Raw name(s)'' column is automatically filled with genome name from the selected VCF file, that column cannot be edited manually.
| |
| − | | |
| − | ==== Import/Export ====
| |
| − | Once a project has been set up, it can be saved using the import/export function. Pressing the export button saves an XML files to the hard drive. This XML file can then be imported to reload the project.
| |
| − | | |
| − | The XML file structure is simple. Each row are stored in ''row'' mark containing every attribute names such as ''group'', ''genome, ''file'' and ''raw_name''. The settings file is formatted as shown in Figure 7.
| |
| − | [[image:mg_basics_xml_settings.png|center|frame|Figure 7: XML file settings]]
| |
| − | | |
| − | | |
| − | '''Note:''' If the user moves the VCF files or changes one of its genotype headers, the XML file will not work anymore. User has to modify ''file'' and/or ''raw_name'' attribute values.<br/>
| |
| − | | |
| − | === Tracks loading ===
| |
| − | Once a multi-genome project has been created, GenPlay creates a meta-genome that is the sum of all the loaded genomes and is capable of converting the coordinates of any data files into the meta-genome coordinates. GenPLay can therefore load data files (tracks) mapped in the coordinates of any of the loaded genomes. Of course, when loading a file, user must specify which genome was used for the mapping.
| |
| − | | |
| − | When loading a track, GenPlay displays a list showing every loaded genome below the window allowing user to load the files. Once the information is entered, GenPlay transforms the coordinates in the file into the coordinates of the meta-genome using the differences information of the specified genome.
| |
| − | | |
| − | === Displaying information ===
| |
| − | In order to display variants information related to genome differences, the user has to create a new layer. To create a new layer, the user has to right-click on the track handler (on the left of the track) of an empty tracks and choose "Add Layer" on the contextual menu (Figure 8). The layer type is "Variant Layer" (Figure 9).
| |
| − | <gallery widths=350px perrow=2>
| |
| − | image:mg_add_layer.png|Figure 8: Add a new layer
| |
| − | image:mg_add_layer_variant.png|Figure 9: Select the variant layer
| |
| − | </gallery>
| |
| − | | |
| − | The next dialog lets the user choose which information to show.
| |
| − | In this example, there is one family group with four members. Genomes have been mapped on the reference genome GRCh37/hg19. It is possible to show on the selected track information such as insertion, deletion and SNPs. User can define the colors (by clicking on the colored squared).
| |
| − | | |
| − | If a data file concerning the father of the family has been loaded, the window looks like the one on Figure 10.
| |
| − | [[image:mg_add_layer_variant_selection.png|center|frame|Figure 10: Multi-genome stripes selection]]
| |
| − | <br/>
| |
| − | | |
| − | Firstly, all stripes related to variants of the selected genome appear (In this case the insertion and the deletion of the father). Secondly, all insertions of the loaded genome are shown as black stripes on all other genomes (black stripes are synchronization marker that have been introduced in the meta-genome to be able to display multiple genome at the same time). The black stripes represent insertions in genome others than in the current genome.
| |
| | | | |
| | == Conversion between NCBI36/hg18 and GRCh37/hg19 == | | == Conversion between NCBI36/hg18 and GRCh37/hg19 == |
In order to set up and manage a Multi-Genome Project in Genplay, please refer to the following sections of the documentation:
This tutorial will explain how to display at the same time tracks mapped on genome assembly NCBI36/hg18 or GRCh37/hg19. In the example, user will be able to see all the modifications on the NCBI36/hg18 genome leading to the GRCh37/hg19 reference genome.
According to bed files provided in this tutorial, the reference genome is GRCh37/hg19. User has to select the mammal clade, the human genome and the Feb 2009 (GRCh37/hg19) assembly as in Figure 2.
The VCF file is about Structural Variants and contains information for chromosomes 1 to 22 and chromosomes X and Y. User can select to load on or more chromosomes by clicking on the settings button next to the assembly name (Figure 3).
To load a file, user has to do a right click on the left part of the track. Then to choose "Load Gene Track", a file chooser appears to select the file given in this tutorial. After having chosen the BED file, a new selection box appears (Figure 13).
This box asks which genome is related to the BED file. Here, user has to choose "Feb 2009 (GFCh37/hg19)" option because the BED file contains information about that genome.
Gene file for GRCh37/hg19 reference has been loaded.
The same operation as loading a gene files for GRCh37/hg19 reference genome. The only step changing is to choose the "Reference genome - hg18 (NCBI36)" option after the BED file selection (Figure 14)
User can navigate into the different chromosomes and visualizes differences between both genomes using the stripes. All genes are perfectly synchronized and are display according to the meta-genome coordinates.
The Figure 15 shows an example of the result of this tutorial. It is possible to see deletions (in red) and insertions (in green) in the NCBI36/Hg18 reference genome compare to the GCh37/Hg19 reference genome.
Chromosome: chr1
Position: 143,822,670
