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Home modified by Yannick Boursin

Yannick Boursin — Wed, 02 Apr 2014 09:08:24 -0000

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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*

Home modified by Yannick Boursin

Yannick Boursin — Wed, 02 Apr 2014 08:55:04 -0000

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-Welcome to your wiki!

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
-
-The wiki uses [Markdown](/p/chipseqanalyzer/wiki/markdown_syntax/) syntax.
-
-[[members limit=20]]
-[[download_button]]

Discussion for Home page

Yannick Boursin — Wed, 02 Apr 2014 08:54:34 -0000

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.
R (designed with 2.15.1)
* bPeaks R module (designed with 1.2=

Python >= 2.6
rpy2 (designed with 2.2.1)
termcolor (designed with 1.1.0)
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 ...)
Any browser

How to run ?

You will need three input files :
Sample 1 (condition 1)
Sample 2 (condition 2)
Control Data
The Genome of your organism
The annotated Genome of your organism with ORF annotation
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 --Output --Output2 --IPData --IPData2 --ControlData --Jaspar

Home modified by Yannick Boursin

Yannick Boursin — Mon, 13 Jan 2014 04:26:11 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Yannick Boursin (admin)