Homer annotatePeaks on genomic regions

Question

[fr]

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

Where my .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

Column6 shows . 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

Answer 1

[bruss]

When I was using HOMER, I created Super Enhancer peak files using their algorithm, however it gave me chromosome identifiers as "1" rather than "chr1", and when input like this it found no peaks. The annotatePeaks requires chromosomes to be formatted as "chr1". Check to make sure thats the case!

[fr]

This is not my case, my chromosomes are written as chr1 too. I really don't understand what's wrong here