[BioC] GenomicAlignments and QNAME collision

[Stefano Calza]

Hi everybody


I am using GenomicAlignments package to read RNAseq pair-end data. The 
problem is that readGAlignmentPairsFromBam, after setting asMates=TRUE 
in BamFile, returns 0 mates.

The reason is that mates have different QNAMEs. Eg:

UNC15-SN850:240:D148CACXX:3:1308:19719:99367/1
UNC15-SN850:240:D148CACXX:3:1308:19719:99367/2

that is the two mates have /1 or /2 at the end.

I wrote a Python (and a cpp) program to fix it...but this takes still 
quite a substantial amount of time on big files.

Does the mating algorithm allow for this? If so how?

Regards

Stefano