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ChipSeqAnalyzer is a python program aimed at discovering transcription factor binding sites, originally in the yeast Candida glabrata. It takes Chip-Seq data as input, and outputs html reports from RSAT / Peak-motifs.

Dependencies

To run ChipSeqAnalyzer, you will need many tools and library installed on your computer.
1. R (designed with 2.15.1)
2. bPeaks R module (designed with 1.2)
* Python >= 2.6
* rpy2 (designed with 2.2.1)
* termcolor (designed with 1.1.0)
3. RSAT (created by J. van Helden, requires licensing, free for academical use)
* peak-motif
* perl / python and many perl modules (follow RSAT manual)
* you may need to install additionnal libraries in order for perl to install its modules (eg. libgd2)
4. Any browser

How to run ?

python ChipSeqAnalyzer -h for help

You will need six input files :
1. Sample 1 (condition 1)
2. Sample 2 (condition 2)
3. Control Data
4. The Genome of your organism
5. The annotated Genome of your organism with ORF annotation
6. Jaspar Matrix

I provided a modified Jaspar Matrix which takes into account YRE elements. Feel free to modify your own or to modify it.

From shell, run :
python ChipSeqAnalyzer.py --Genome your genome --Output bPeaks output file name for condition 1 --Output2 bPeaks output file name for condition 2 --IPData data for sample 1 --IPData2 data for sample 2 --ControlData control data --Jaspar your jaspar matrix