This is the old version of
the documentation: New
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.
[general options] [-A | B | C | D
This command performs 4 separate tasks labeled as A,B,C & D:
i.e. a common use: analyzeChIP-Seq.pl
Factor-ChIP-Seq/ hg18r -i Input-ChIP-Seq -focus -A
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
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
-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