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ACT Integrated Example: Whole-Genome ChIP-Seq experiments
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:
see http://info.gersteinlab.org/ACT_IntegratedExample
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
 
*Saturation
 
Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.

Latest revision as of 17:46, 10 September 2010

ACT Integrated Example: Whole-Genome ChIP-Seq experiments

see http://info.gersteinlab.org/ACT_IntegratedExample

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