Hello,

I would like to get positions of motifs (start and end positions) for the motifs found in every peak using annotatePeaks.pl of Homer. I tried the following:

annotatePeaks.pl ad_close.bed Aque1.31 -m knownResults/*.motif -gff3 Aqu2.1_Genes.gff3  -mbed motifs.bed > motifs.tsv

The output file motifs.bed has positions for the peaks present in each contig:

Contig13470 239433  239445  MYB3R4(MYB)/Homer   8.288071    +

Contig13464 37847   37859   MYB3R4(MYB)/Homer   7.195835    +

Contig13462 264324  264336  MYB3R4(MYB)/Homer   9.530264    -

Contig13036 3430    3442    MYB3R4(MYB)/Homer   7.475983    -

but I want the output to have positions for the motifs found in each peak (by peak id) , I tried the option -mpeak instead of -mbed and only changes the format of the output, I also tried with a peak file as input instead of bed file. Any ideas?

Thanks