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?