Hi
I have use FIMO to find a particular set of 4TF motifs on my chip-seq peaks, the output of FIMO describes coordinates within fasta sequence, does anyone have experience in taking FIMO GFF results and use it to re-annotate peak coordinates to know which one has a particular motif enrichment for one TF but not for another? in a large set of coordinates.
Thanks
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carlosalfonsogonzalez6 •
If you have peak file in 3-column bed format, you can try the following
cat fimo.txt | grep -v start | cut -f2,3 | tr '|' '\t' | awk -F'\t' '{print $3 "\t" $4 "\t" $5 "\t" $1 "\t" $2}' | sort -k1,1V -k2,2n | intersectBed -a - -b peakFile.bed -wao | cut required fields
P.S. Different versions of FIMO gives slightly different number of columns in it's output. Be careful and see what you are selecting.
Thank you very much, this is really helpful, I did realize that fimo has a command to give specific regions of the initial bedfile.
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