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