Question: DiffBind with paired-end ChIP-seq data
0
gravatar for shen_
4 weeks ago by
shen_0
shen_0 wrote:

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 • 39 views
ADD COMMENTlink written 4 weeks ago by shen_0
Answer: C: DiffBind with paired-end ChIP-seq data
0
gravatar for shen_
4 weeks ago by
shen_0
shen_0 wrote:

I solved this by setting "minOverlap = 1".

data$config$singleEnd <- F
data <- dba.count(data,minOverlap=1,bUseSummarizeOverlaps=T)
ADD COMMENTlink written 4 weeks ago by shen_0
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