Tutorials

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

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.

Load the file

Start by downloading download the file from the tutorial directory here. You can also the refSeq gene annotation file here. 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.

Figure 1: Load Menu

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.

Figure 2: Load Fixed Window Track Menu

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.

Isolate Peaks

This step consist in removing the background noise from the track so just the peaks remain.