Hi,
using:
flagL <- scanBamFlag(isDuplicate=FALSE, isNotPassingQualityControls=FALSE)
ParamL <- ScanBamParam(flag = flagL, what="seq")
BAM <- readGAlignmentPairs(file.bam,use.names = T, param = ParamL)
I don't get anything in mcols(BAM)$seq ... there is no metadata whatsoever.
But If I use readGAlignments() function It works fine.
Does readGAlignmentPairs() support importing of actual sequences? I don't get any error, there is just nothing read in.
If it does, how can I make it work, if it doesn't what is the suggested workaround?
Thank you!
Lovro
using:
flagL <- scanBamFlag(isDuplicate=FALSE, isNotPassingQualityControls=FALSE)
ParamL <- ScanBamParam(flag = flagL, what="seq")
BAM <- readGAlignmentPairs(file.bam,use.names = T, param = ParamL)
I don't get anything in mcols(BAM)$seq ... there is no metadata whatsoever.
But If I use readGAlignments() function It works fine.
Does readGAlignmentPairs() support importing of actual sequences? I don't get any error, there is just nothing read in.
If it does, how can I make it work, if it doesn't what is the suggested workaround?
Thank you!
Lovro