Difference between revisions of "Tutorials"

From GenPlay, Einstein Genome Analyzer

Latest revision as of 11:18, 22 August 2014

The following tutorials aim to give you some of the basic concept on the track manipulation techniques.

1 ChIP-Seq Analysis
2 TimEX Analysis
3 Multi-Genome Analysis
4 How to Create a VCF File From a Chain File

ChIP-Seq Analysis

The objective of the ChIP-Seq Tutorial is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment.

TimEX Analysis

The TimEX Tutorial illustrates how GenPlay can be used to show timing of replication profiles.

Multi-Genome Analysis

The GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial explains how to use the multi-genome functionality of GenPlay.

It shows how data aligned on hg38 and hg19 can be displayed simultaneously and compared using GenPlay Multi-Genome

Note: Here is a version for the comparison of hg18 and hg19: Multi-Genome Tutorial.

How to Create a VCF File From a Chain File

The goal of this tutorial is to show how to generate a VCF file such as the one used in the GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial from a Chain file that can be downloaded from the UCSC genome browser website.

Retrieved from "http://genplay.net/wiki/index.php?title=Tutorials&oldid=2004"

@@ Line 2: / Line 2: @@
 == ChIP-Seq Analysis ==
-'''Goal:''' First, isolate the peaks from the data generated from a ChIP-Seq experiment. Then generate a list of genes that have a peak in their promoter and associate for each promoter the score of the peak summit.
+The objective of the [[ChIP-Seq Tutorial]] is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment.
-=== Load the file ===
+== TimEX Analysis ==
-The first thing to do is to download the file CHiP-Seq file and the refSeq gene annotation file from the tutorial directory here.
+The [[TimEX Tutorial]] illustrates how GenPlay can be used to show timing of replication profiles.
-After that you can start GenPlay from the Web Start link that is located on top of this page. The 1 GB link is enough for this tutorial.
-For this experiment we're going to work only on the first chromosome so the loading is shorter and the amount of memory needed is smaller too.
-We first want to know if the position between the two strands are shifted.
-For that we need to load the file twice, on the 3' and on the 5' separately.
-[[image:tutorial1_empty_track_menu.png|left|thumb|100px|Figure 1: Load Menu]]
+== Multi-Genome Analysis ==
-You need to right click on the track  handler of the 1st row, in order to open the menu that will allow you to load the track (figure 1). Select the Load Fixed Window Track option.
+The [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] explains how to use the multi-genome functionality of GenPlay.
-<br style="clear: both" />
-[[image:tutorial1_Load_FWT_menu.png|right|thumb|100px|Figure 2: Load Fixed Window Track Menu]]
+It shows how data aligned on hg38 and hg19 can be displayed simultaneously and compared using GenPlay Multi-Genome
-After selecting the file, a option window is going to prompt you to enter some information. You can keep the default name for the track. You need to choose a window size of 100 base pair, and sum for the score calculation. Please refer to the documentation page for more information about these options. You can keep the default data precision. But we need to select a strand. Let's start with the 5' strand. You will also need to select the 1st chromosome. To do so, click on the "Modify Selection" button on the bottom right part of the screen and then uncheck all the chromosomes but the first. The figure 2 shows how the screen should like before you click on the OK button.
-<br style="clear: both" />
-The operation need to be repeated for the 3' strand. Once the tracks are loaded you can modify the Y axis by right clicking on the track handler and selecting the "Set Y Axis" option. Set the maximum to 50. Now that the two track are loaded we can graphically determine how much the 2 strands are shifted. Select a peak, zoom on it with the mouse wheel and check how far the summits of the same peak on the 5' and the 3' strands are. Verify that this value is the same. When you're sure about the value divide it by to and note this result. We notice that the summits are 200 bp away so the shifting value is 100 bp (meaning that the 5' is shifted 100 bp forward and the backward strand is shifted 100 bp backward).
+'''Note:''' Here is a version for the comparison of hg18 and hg19: [[Multi-Genome Tutorial]].
-We need to load the file one last time. This time the loading screen should look like on the figure 3.
+== How to Create a VCF File From a Chain File ==
-[[image:tutorial1_Load_FWT_menu2.png|right|thumb|100px|Figure 3: Load Fixed Window Track Menu, both strands]]
+The goal of [[How to Create a VCF File From a Chain File|this tutorial]] is to show how to generate a VCF file such as the one used in the [[GRCh37/hg19 GRCh38/hg38 Multi-Genome Tutorial]] from a Chain file that can be downloaded from the UCSC genome browser website.
-=== Isolate Peaks ===
-This step consists in removing the background noise from the track so just the peaks remain.
-To do so, right click on the