HOMER findMotifsGenome.pl to get the location of the motifs

Question

[bsharmi6]

Hello,

I need to find the location of known motifs from ChIP-seq data. I used HOMER findMotifsGenome.pl but I have a question on calculating the exact location. The output file from HOMER contains the columns: Peak/Region ID Offset from the center of the region Sequence of the site Name of the Motif Strand Motif Score (log odds score of the motif matrix, higher scores are better matches)

So in order to get the motif location should I do (Region Start + Region Center + Offset from center)?

I am sorry I am confused on how to use the offset parameter.

Thank you very much, Sharmi

[nicolas.soriano]

Hello,

Did you get an answer ?

I'm looking for the same information...

Thanks

[Nitin Narwade]

I am not sure about this output format of homer, perhaps this is an older version homer of output, explained in the question. However, I use fimo (tool from meme-suite) to check the motif occurrence in the given sequences. it will retain the locations of a given motif in the target sequences.