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Back to Elementolab/ChIPseeqer_Tutorial


This ChIPseeqer module requires installation of our MyScanACE program (Elemento lab reimplementation of ScanACE). To install MyScanACE, please take a look at the ChIPseeqer installation page (bottom)

To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH variable. Read How to set the CHIPSEEQERDIR variable.

You also need to set the $PERLMODULESDIR variable.

1. To find all peaks that have a match to the Bcl6b PBM motif, run the command:

ChIPseeqerMotifMatch --targets=peaklist.txt --motifname=Bcl6b --genome=DATA/hg18/WG/wg.fa

2. To find all peaks that have a match to "TCCTAGA" motif sequence, run the command:

ChIPseeqerMotifMatch --targets=peaklist.txt --motifseq="TCCTAGA" --genome=DATA/hg18/WG/wg.fa


--motifname=STR # the (JASPAR or PBM) name of the motif to look for (e.g., STAT3)
--motifseq=STR  # the sequence of the motif to look for (e.g., TCCTAGA, [TA]CGC[CG])
--c=FLOAT       # to set the motif score threshold, in standard deviations below the average. -c 1 is the default, use -c 0 for higher affinity matches.

This program requires a human genome sequence (wg.fa above).

3. See the results

The output of the program is simply a subset of the input; the program also adds two columns: the position in the peak region of the best motif match and the relative position (%) of that match in the peak (50% means the motif is right in the middle of the peak region).

chr10	100018179	100018528	254	72.6
chr10	100221989	100222321	45	13.5
chr10	10127166	10127611	174	39.0
chr10	101506149	101506412	43	16.3
chr10	101595511	101596200	678	98.3

4. What can I do next ?

Once you get a list of peaks saved in a text file, you can find the genes associated with these peaks using Elementolab/ChIPseeqer_Annotate.

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