I have chip-seq data and used MACS2 to find peaks (genomic regions enriched for methylation). now I want to find the motifs. I found a tool called "DREME". but the input file for that is .fasta format and what I have is .broadpeak file. do you know how to use DREME and .broadpeak file?
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alirezamomeni707 •
1 answer
Have you read the tutorial?
"DREME works best with lots of short (~100bp) sequences. If you have a couple of long sequences then it might be beneficial to split them into many smaller (~100bp) sequences. With ChIP-seq data we recommend using 100bp regions around the peaks."
Have you looked at what is inside the broadpeak file? - it contains positions, you may need to create a fasta file for the positions
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