DiffBind Count reads from paired end bamfiles

Question

[g.persic1991]

Hi guys... I have a (URGENT !!!!) question about how to use dba.count when I have a Paired-End bam files...

For Single-end data processed up to now, after create a consensus peak,

dbob.consensus <- dba.peakset(dbObj, consensus = DBA_CONDITION, minOverlap=0.5)
consensus <- dba.peakset(dbob.consensus, bRetrieve=TRUE,
                             peaks=dbob.consensus$masks$Consensus, minOverlap=1)

I used dba.count with below command

dbObj_01_TMM <- dba.count(dbObj, peaks=consensus, bUseSummarizeOverlaps=TRUE, minOverlap=1)

Now my question is, can I use these code also for BAM PE data???

If not, can you suggest me how to do???

thanks in advance Giuseppe

Answer 1

[Rory Stark]

If you look at the help page for dba.count(), it shows some configuration options that are used when bUseSummarizedOverlaps=TRUE. Specifically, you can set

`myDBA$config$singleEnd <- FALSE`

before calling dba.count() to use paired-end mode.

Note that in the version being released this week (October 28), the default is no bUseSummarizedOverlaps=TRUE, and DiffBind will automatically detect single-end/paired-end mode.