DiffBind with paired-end ChIP-seq data
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shen_ • 0
@shen_-22158
Last seen 5.1 years ago

I tried to count reads around peak set based on paired-end ChIP-seq data. But I don't want to get a consensus peak set. So I add "peaks=NULL" according to the document of DiffBind.

Here is my code:

> data$config$singleEnd <- F
> data <- dba.count(data,peaks=NULL,bUseSummarizeOverlaps=T)
Error in dba.count(data, peaks = NULL, bUseSummarizeOverlaps = T) : 
  DBA object must contains only counts
software error • 462 views
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Entering edit mode
shen_ • 0
@shen_-22158
Last seen 5.1 years ago

I solved this by setting "minOverlap = 1".

data$config$singleEnd <- F
data <- dba.count(data,minOverlap=1,bUseSummarizeOverlaps=T)
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