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Old 03-18-2014, 11:03 AM   #36
Senior Member
Location: US

Join Date: Aug 2013
Posts: 123

I couldn’t find your original problem, but if I remember correctly, your summarizeOverlaps step didn’t work. And you did something like:

flag <- scanBamFlag(isNotPrimaryRead=FALSE, isProperPair=TRUE)
param <- ScanBamParam(flag=flag)
gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union", ignore.strand=TRUE, single.end=TRUE, param=param)

I guess you have single end data, so try:
flag <- scanBamFlag(isNotPrimaryRead=FALSE, isProperPair=NA)
The following flag line is for paired end data:
flag <- scanBamFlag(isNotPrimaryRead=FALSE, isProperPair=TRUE)

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