use Homer to annotation region of ChIP-seq peaks.

Question

[mikysyc2016]

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.

Answer 1

[Benn]

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.