Question: use Homer to annotation region of ChIP-seq peaks.
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gravatar for mikysyc2016
9 months ago by
mikysyc201630
mikysyc201630 wrote:

Homer (http://homer.ucsd.edu/homer/ngs/annotation.html) can be used to do ChIP-seq regions annotation. I do not use homer to do the whole ChIP-seq analysis. So i do not get homer peak files. I use macs2 to do peak calling and get bed file. But the file did not contain strand column. So I want know whether this strand is necessary.Once i use the bed file from macs2 and use Homer to do region annotation. The output fie will include the strand colume, but all the strands show "+". Does this right? Thanks.

chip-seq • 562 views
ADD COMMENTlink modified 9 months ago by b.nota6.4k • written 9 months ago by mikysyc201630
1
gravatar for b.nota
9 months ago by
b.nota6.4k
Netherlands
b.nota6.4k wrote:

You only need the bed file produced by macs2 for homer. They need to contain the coordinates of the peaks (chr, start, end position), followed by the peak name (which is given by macs2).

The output will indeed only contain "+" for each peak.

ADD COMMENTlink modified 9 months ago • written 9 months ago by b.nota6.4k
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