Preparing a .bed for Homer annotation

Question

[giroudpaul]

Hello

I have a 5 columns bed file with Chr | Peak Start | Peak End | Unique ID | Score

I want to annotate this Bed file using HOMER.

However, and this seem logical to me, homer require a 6th column with the strand information.

I have seen some solutions on how adding a strand column with only + in it, however I am wondering if this makes sense to do this, as the annotation may not be the same depending on the strand.

So my question is, is there a way to add the correct strand information for each peaks, is there a peak calling setting for this (I used macs14, and I didn't found an option that seems to do this) ?

Thanks

[Medhat]

In BED files, a dot "." can be used successfully with many tools to represent a "NULL" value for strand (this defaults to "+" when used with some tools), Did you tried to use dot?

Answer 1

[jiab]

annotatePeaks.pl in the HOMER package seems to ignore strand information anyway.

I posted about it here: Strand information when doing peak annotation with HOMER