Elementolab/ChIPseeqerMotifMatch
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| --motifseq=STR # the sequence of the motif to look for (e.g., TCCTAGA, [TA]CGC[CG]) | --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. | --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. | ||
| - | --output=all # will show all motif matches, with their position within peaks as well as orientation | ||
| This program requires a human genome sequence (wg.fa above). | This program requires a human genome sequence (wg.fa above). | ||
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Back to Elementolab/ChIPseeqer_Tutorial
ChIPseeqerMotifMatch
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
Options:
--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.
