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Old 11-11-2016, 08:26 AM   #1
Lovro
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Location: Slovenia

Join Date: Mar 2015
Posts: 19
Default genomicAlignments package in R

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
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