Homer annotatePeaks on genomic regions
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Entering edit mode
2.4 years ago
fr ▴ 170

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?

homer ChIP-Seq annotatepeaks • 876 views
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Entering edit mode
2.4 years ago
bruss ▴ 30

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!

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Entering edit mode

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