Multi-Genome Tutorial

Getting started
In order to set up and manage a Multi-Genome Project in Genplay, please refer to the following sections of the documentation:
 * Loading a Multi Genome Project
 * Loading a Variant Layer
 * Variant Layer operations

Description
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.

Files

 * XML settings file
 * VCF file
 * Indexed VCF file (Tabix)
 * Refseq BED file for GRCh37/hg19
 * Refseq BED file for NCBI36/hg18

Project name
User must choose a name for a new project; here the name is GenPlay-MG – Reference genome tutorial (Figure 1).

Project assembly
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.

Chromosome selection
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).

VCF Loading
Manually To load VCF files, users must first fill the column lists and then select from the list the appropriate data. The VCF Loader appears after clicking on the Edit button from the welcome screen. The bottom left part of the VCF Loader contains the Column list edition section. User has to select a column and click on Edit button in order to show the associated list. Only one VCF file is going to be loaded for this tutorial. The VCF file contains differences between the reference genome NCBI36/hg18 and the reference genome GRCh37/hg19.

Group column This tutorial compares reference genome; a generic group name can be Reference genome. On the Group name list editor, user clicks on the plus button to show the input text box and fills it (Figure 4). The Group name list editor should looks like the Figure 5 below. Once the values has been added to the list, it can be saved by closing the "Group name list editor window" value:  Reference genome

Type column This field cannot be edited by the users. The provided VCF file is a Structural Variant type, user therefore has to choose SV (Figure 8). value: SV

File column Once the VCF file is downloaded, user has to open the File list editor, user clicks on the plus button to show the file chooser dialog and choose the VCF file according to its location. value: VCF path

Raw name(s) column The raw name list is automatically filled. In the case of this tutorial there is only one genome: NCBI36 (Figure 10). value: NCBI36 Again, value is saved by closing the windows

Import XML settings In order to set the project with ease, user can import the settings using the XML file above. Please be careful about the VCF path, user must changes it directly on the xml file if he wants to use the import function.

Conclusion Finally, the screen should be like the one on Figure 11.

Conclusion
The welcome screen should finally be similar to the Figure 12. The "Create" button will create the project and will run the synchronization.

GRCh37/hg19 genes loading
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.

NCBI36/hg18 genes loading
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)

Conclusion
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