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