I'm trying to annotate whole genomic regions, whose coverage I have computed before, from
.bed files. To do so I'm using
annotatePeaks.pl myfile.bed mm10 -noadj -fragLength 130 -annStats my_stats.txt > output.txt
.bed file has the correct format:
BED files should have at minimum 6 columns (separated by TABs, additional columns will be ignored) Column1: chromosome Column2: starting position Column3: ending position Column4: Unique Peak ID Column5: not used Column6: Strand
. in my case.
However, while I care about what genomic features lie within those bins, Homer says that it doesn't find any peaks whatsoever. But looking at the input columns, the positions should be enough to do the annotation right?
How can I solve this?
Thanks a lot in advance