Question: Motif frequency for each interval
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gravatar for jmckow1
3.8 years ago by
jmckow10
United States
jmckow10 wrote:

I would like to search Chip-seq intervals (BED, bigwig, ect) for the frequency of a preset motif. Ideally outputting new interval files, each containing intervals that posses the same number of motifs. Please reply with any recommendations as to the simplest way to accomplish this. Thank You.

blast motif sequence meme homer • 977 views
ADD COMMENTlink modified 3.7 years ago • written 3.8 years ago by jmckow10

Do you want to search a bed file with a known motifs and get the coordinates of matches ?

ADD REPLYlink written 3.8 years ago by geek_y10k

I want to "rank" each bed interval according to number of short motifs present in that interval. Then I would like to split the original BED file into subsets based on "rank" of interval. Right now to accomplish this I getFastaFromBed (Bedtools) and then I use a script I found searching BioStars (https://github.com/Farhat/patt_search). This approach seems a bit cumbersome, someone else may have a better way.

ADD REPLYlink written 3.7 years ago by jmckow10
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