Entering edit mode
8 weeks ago
EdisonJ
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0
I started with a ChIP‑seq peak BED file and ran HOMER to find my target motif, using HOMER’s PWM to get motif-level details for each peak. I also extracted the peak sequences from hg38.fa and ran FIMO with a MEME-format motif matrix, which gave me a TSV of motif hits per peak. Now I want to convert those motif hits into BED (or bigBed) files and load them as a track in a genome browser (e.g., IGV or JBrowse). How can I do?
Show an example of the data. Converting this to BED format should not be difficult, as long as you have the chromosome names and starts available.
TSV file from fimo not that hard to back to bed file, because the tsv file give the location of each peak. BUT, the homer result don't show exactly location of each peak. How to trace homer's result back.
Sounds like "finding instances of specific motifs" section from the page below is what you are after:
http://homer.ucsd.edu/homer/ngs/peakMotifs.html