How to import a BED file to ChIPseeker in order to visualize genome coverage plot?
Could you please explain how to connect the ATAC-Seq peak results discovered by DiffBind to be imported to ChIPseeker to get CHIP peaks coverage plot?
For example, I have the following bed file.
chr14 54222322 54222722 m1
chr5 32077186 32077586 m2
chr6 108688361 108688761 m3
chr8 11798255 11798655 m4
How can i visualize CHiP peak coverage plot in mouse (Mus musculus) genome using ChIPseeker?
1 answer
You can do:
library(ChIPseeker)
peak <- readPeakFile("yourfile.bed")
covplot(peak)
By the way, I think that in the importing process your BED file is converted to 1-based coordinates (so 1 bp is added to the start of the peaks), so take that into account (because what you call peaks/BED files may or may not be 0-based).
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