GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial - Revision history

Julien: /* Adding DNA Sequence Layers */

2014-06-27T20:12:41Z

‎Adding DNA Sequence Layers

2014-06-27T20:09:05Z

‎Displaying SNPs, Insertions and Deletions

2014-06-27T20:08:06Z

‎Automatically

2014-06-27T20:07:22Z

‎Manually

2014-06-27T20:05:16Z

‎Selecting the Reference Assembly

2014-06-27T20:04:32Z

‎Selecting the Reference Assembly

2014-06-27T20:04:12Z

‎Selecting the Reference Assembly

2014-06-27T20:03:10Z

2014-06-27T20:02:44Z

2014-06-27T19:56:43Z

@@ Line 96: / Line 96: @@
 == Adding DNA Sequence Layers ==
-We are going to insert two layers. To do so, right click on the track handler of track 1 and select the ''Insert'' option of the contextual menu. Repeat this operation a second time to insert another layer.
+We are going to insert two blank tracks. To do so, right click on the track handler of track 1 and select the ''Insert'' option of the contextual menu. Repeat this operation a to insert a second empty track.
-Now click on the first track handler and select ''Add Layer(s)''. The select the hg38 DNA file downloaded at the beginning of the tutorial. When asked what was the genome used for the alignment select hg38.
+Now click on the first track handler and select ''Add Layer(s)''. Then, select the hg38 DNA file downloaded at the beginning of this tutorial. When asked what was the genome used for the alignment, select hg38.
 Repeat this operation for the hg19 DNA sequence file. Make sure to select hg19/Maternal allele as the genome used for the alignment.
-Please note that you might need to zoom in in order to visualize the DNA sequences. This can be easily done by using the mouse wheel.
+You should now be able to visualize DNA sequences. Please note that you might need to zoom-in in order to visualize the DNA sequences. This can be easily done by using the mouse wheel.
 The final result of this tutorial is shown in figure 12.
 [[image: hg19-38_tutorial_final_result.png|center|frame|Figure 12: Final Result]]

@@ Line 65: / Line 65: @@
 [[image: hg19-38_tutorial_add_variant_layer1.png|center|frame|Figure 4: Add Variant Layer]]
-Then click on the ''SNPs' check box (figure 5).
+Then click on the ''SNPs'' check box (figure 5).
 [[image: hg19-38_tutorial_add_variant_layer2.png|center|frame|Figure 5: VCF Select Variants to Add]]

@@ Line 56: / Line 56: @@
 ==== Automatically ====
-You can automatically setup the multi-genome project by clicking on the ''Import Config'' button at the bottom of the project screen and select the XML file downloaded earlier. You have to make sure that the VCF file and the XML file are in the same directory when you choose this option.
+You can automatically setup the multi-genome project by clicking on the ''Import Config'' button at the bottom of the project screen and selecting the XML file downloaded earlier. You have to make sure that the VCF file and the XML file are in the same directory when you choose this option.
 == Displaying SNPs, Insertions and Deletions ==

@@ Line 45: / Line 45: @@
 ''Nickname column''
-The nickname can be used do differentiate samples with having the same raw name. In this example we can keep the default nick name.
+The nickname can be used do differentiate samples having the same raw name. In this example we can keep the default nick name.
 ''Group column''

@@ Line 27: / Line 27: @@
 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).
+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'' button (figure 2).
 [[image: hg19-38_tutorial_chromo_selection.png|center|frame|Figure 2: Project Chromosomes]]

@@ Line 25: / Line 25: @@
 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).
+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).

@@ Line 1: / Line 1: @@
 '''Goal''': This tutorial illustrates how the multi-genome mode of GenPlay can be used to simultaneously display data aligned on different reference genomes. 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.
+'''Prerequisite:''' 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.
 '''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.

← Older revision		Revision as of 20:02, 27 June 2014
Line 1:		Line 1:
−	'''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.	+	'''Goal''': This tutorial illustrates how the multi-genome mode of GenPlay can be used to simultaneously display data aligned on different reference genomes. 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.		'''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.

@@ Line 91: / Line 91: @@
 [[image: hg19-38_tutorial_hg19_ref.png|center|frame|Figure 10: Select hg19]]
-The final result of this tutorial is showed in figure 11.
+The result of this step is showed in figure 11.
-[[image: hg19-38_tutorial_final_result.png|center|frame|Figure 11: Final Result]]
+[[image: hg19-38_tutorial_gene_layers_added.png|center|frame|Figure 11: Gene Layers]]