DiffBind remove Unplace Chromosome (chrUn)

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mdidish ▴ 10

@cbee3b30

Last seen 4 months ago

France

Hello I am using DiffBind for ATAC-Seq analysis. I would like to remove peaks located on random chromosomes and chrUn (Unplace Chromosome). I found the argument bRemoveRandom = T in the dba() function, nothing for chrUn.

So I have two questions:

how to remove all peaks locating on chrUn_...?
when I try epic.dba2 <- dba(DBA = epic.dba, bRemoveRandom = T), I have the same number of peaks in both dba objects. Does this argument only work when creating the dba object?

Best,

edit: even when I create dba object with dba(sampleSheet = "./sample.csv", minOverlap = 0.20, bRemoveRandom = T), I still have chr1_KI270709v1_random and other random chromosomes in the dba object

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ADD COMMENT • link 4 months ago mdidish ▴ 10

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Looking at the dba() function, which points to pv.model() and then to pv.peakset(), I found this:

for(i in c(1:22,"X","Y")) {
    ch = sprintf("chr%s_random",i)

but the random chromosomes in my dataset are of the format chr1_KI270710v1_random.

ADD REPLY • link 4 months ago mdidish ▴ 10

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