Multi-Genome Tutorial - Revision history

Julien: /* Getting started */

2014-06-25T17:56:41Z

‎Getting started

2014-04-23T20:51:12Z

‎Manually

2014-04-23T20:50:04Z

‎Manually

2014-04-23T20:27:03Z

‎Chromosome selection

2014-04-23T20:26:16Z

‎Project name

2014-04-23T20:22:48Z

‎VCF Loading

2014-04-23T20:19:41Z

‎VCF Loading

2014-04-23T20:18:51Z

‎Manually

2014-04-23T20:18:35Z

‎VCF Loading

2014-04-23T19:59:22Z

‎Conversion between NCBI36/hg18 and GRCh37/hg19

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 * [[Documentation#Loading a Variant Layer|Loading a Variant Layer]]
 * [[Documentation#Variant Layer Operations|Variant Layer operations]]
 == Conversion between NCBI36/hg18 and GRCh37/hg19 ==

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 Since this tutorial is about comparing reference genomes; a generic group name can be ''Reference genome''.
-Click on the ''Group 1'' text of the ''Group'' column and then click and the pencil to edit the name of the group (Figure 4).
+Click on the ''Group 1'' text of the ''Group'' column and then click on ''Add...'' to enter group (Figure 4).
-The ''Group name list editor'' should looks like the Figure 5 below.
+The ''Group name 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"
+Once the values has been added to the list, it can be saved by closing the "Group name editor window"
 ''value:'' ''' Reference genome'''

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 ====== Manually ======
 Next we need to setup a multi-genome project. To do so, click on the ''Multi Genome Project'' radio button at the bottom of the screen and click on ''Select VCF''.
+Click on the ''Add...'' label of the File column to select the VCF file to load. Select the VCF downloaded earlier. 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''.
+Since this tutorial is about comparing reference genomes; 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).
+Click on the ''Group 1'' text of the ''Group'' column and then click and the pencil to edit the name of the group (Figure 4).
 The ''Group name list editor'' should looks like the Figure 5 below.

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 ===== Chromosome selection =====
-The VCF file contains Structural Variants for chromosomes 1 to 22 and chromosomes X and Y. The list of chromosomes available in the project can be set by clicking on the settings button (with a toolbox image) next to the assembly name (Figure 3).
+The VCF file contains Structural Variants for chromosomes 1 to 22 and chromosomes X and Y. The list of chromosomes available in the project can be set by clicking on the settings button (toolbox image) next to the assembly name (Figure 3).
 [[image:mg_hg18tohg19_chromosome_chooser.png|center|frame|Figure 3: Chromosome chooser]]

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 ==== Project settings ====
 ===== Project name =====
-The first thing to do is choose a name for the new project; here the name is ''GenPlay-MG – Reference genome tutorial'' (Figure 1).
+The first thing to do is to choose a name for the new project; here the name is ''GenPlay-MG – Reference genome tutorial'' (Figure 1).
 [[image:mg_hg18tohg19_project_name.png|center|frame|Figure 1: Project name]]

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-''''' Group'' column '''
+''Group column''
 This tutorial compares reference genome; a generic group name can be ''Reference genome''.
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 </gallery>
-======= Genome column =======
 The genome name is an Alias for the selected raw name. In this tutorial, the genome name is going to be '''Hg18'''.
 On the ''Genome name list editor'', user clicks on the plus button to invoke the input text box and fills it (Figure 6).
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 </gallery>
-======= 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).
@@ Line 76: / Line 80: @@
-======= File column =======
+''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.<br/>
 ''value:'' '''VCF path'''
 [[image:mg_hg18tohg19_file_editor.png|center|frame|Figure 9: VCF File editor]]
-======= 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).<br/>
 ''value:'' '''NCBI36'''

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 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. Click on the ''Add...'' label of the File column to select the vcf file to load. Select the VCF download ealier. 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).