GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial

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.

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

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).

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).

Figure 2: Project Chromosomes

Selecting the Reference Assembly

Setting the Multi-Genome Parameters

Displaying SNPs, Insertions and Deletions

Displaying Gene Annotation Layers