How to import a BED file to ChIPseeker in order to visualize genome coverage plot?

Question

[mrj]

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?

Answer 1

[Papyrus]

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).

[mrj]

Thank you for the answer and the insight into BED file coordinates. This worked.

[Papyrus]

glad to help! ;)