FIMO output analysis

Question

[carlosalfonsogonzalez6]

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

Answer 1

[venu]

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.

[carlosalfonsogonzalez6]

Thank you very much, this is really helpful, I did realize that fimo has a command to give specific regions of the initial bedfile.