How to get Motif positions by peak (not by Chromosome) using Homer annotatePeaks.pl ??
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19 months ago
carina2817 ▴ 20

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

Homer annotatePeaks Motif positions peakid • 556 views
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