Question: Preparing a .bed for Homer annotation
1
gravatar for giroudpaul
4.1 years ago by
giroudpaul70
European Union
giroudpaul70 wrote:

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

bed annotatepeaks homer • 2.2k views
ADD COMMENTlink modified 2.6 years ago by jiab30 • written 4.1 years ago by giroudpaul70

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?

ADD REPLYlink written 3.1 years ago by Medhat8.6k
0
gravatar for jiab
2.6 years ago by
jiab30
jiab30 wrote:

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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by jiab30
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