Software for motif discovery and ChIP-Seq analysis

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ChIP-Seq Analysis: Analyzing a ChIP-Seq experiment with one command

Even I don't like typing the same commands over and over again.  The following command performs the standard set of analysis commands so that you can do better things while your data is processed.

analyzeChIP-Seq.pl <Tag Directory> <genome> [general options] [-A | B | C | D sub-program options]

i.e. a common use: analyzeChIP-Seq.pl Factor-ChIP-Seq/ hg18r -i Input-ChIP-Seq -focus -A factor_alignment_file.bed factor_alignment_file2.bed

This command performs 4 separate tasks labeled as A,B,C & D:

A. Runs makeTagDirectory to parse alignment files, set up the tag directory, and performs basic QC such as tag auto correlation and checks for sequence bias.
B. Runs make makeUCSCfile and findPeaks to generate UCSC Genome Browser files and peak files for the experiment.
C. Runs findMotifsGenome.pl to determine enriched motifs in your ChIP-Seq peaks.
D. Runs annotatePeaks.pl to generate an annotated peak file and performs GO analysis on genes found near the peaks.

As output, this program will create standard files in the "Tag Directory" including an "index.html" file that links you to each of the output files. 

There are a couple of general options that can be used with analyzeChIP-Seq.pl:

-i <input tag directory> : "Tag directory" to use as a control for peak finding.
-size <#> : Force this peak size for analysis (default is "auto" for peak finding, 200 bp for motif analysis and 50 bp for focused peak analysis)
-focus : This will find enriched motifs in 90% focused peaks using only +/- 25 bp of sequence, useful for identifying the primary motif bound by the factor.
-enhancer : This will set the peak size to "-size 1000" and only perform motif analysis on peaks > 3kb from the TSS.

To specifically tailor the options used by the sub-programs, first enter the "general options" you want above, then enter "-A" followed by the options you want passed to the sub-programs.  For example, the most used sub-program option I use is the following:

"-A s_1_eland_result.txt" - this passes the alignment file to the makeTagDirectory program so that it will be used to make the Tag Directory.

If you've already made a tag directory, no need to use the "-A blah blah" option.  In similar fashion, to tell the motif finding to check motifs of length 10, 11, and 12, add "-C -len 10,11,12" to the end of the command.

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