ACT IntegratedExample

From GersteinInfo

ACT Integrated Example: Whole-Genome ChIP-Seq experiments

Here we describe how to use ACT on a set of two large example files from ChIP-Seq experiments.

To begin, download the signal files (from Gerstein Lab's PeakSeq project) here:

http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/PolII/Signal_Maps/PolII/

http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Results/STAT1/Signal_Maps/STAT1/

These are zipped signal files for PolII and Stat1. After unzipping the files for each transcription factor, it is useful to cat the signal tracks for the individual chromosomes together so that all the signals are in only two files. In this walkthrough they will be referred to as PolII.sgr and Stat1.sgr.

• Aggregation

• Correlation

It is necessary to convert the signal tracks from sgr to wig format. A script which does this can be found here:

http://act.gersteinlab.org/sgr2wig.pl

The resulting correlation matrix can be plotted in R:

• Saturation

It is necessary to convert the wig files to bed files without a "signal" component. The following script takes wig files and converts them into bed files, with coordinates representing the regions of the signal track which are above a certain threshold (in this case 0).

http://act.gersteinlab.org/wig2bed.pl

Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.