Preparing a .bed for Homer annotation
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6.5 years ago
giroudpaul ▴ 70

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

Homer annotatePeaks Bed • 3.4k views
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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?

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5.0 years ago
jiab ▴ 60

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

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