[BioC] GenomicAlignments and QNAME collision

[Valerie Obenchain]

Hi Stefano,

No, the current mate-pairing doesn't handle the trailing values. I will 
implement this and post back when it's done.

For reference, where did you download your bam files or what application 
outputs QNAMEs in this format? I'd like to have some for test data.


Thanks.
Valerie


On 05/08/14 08:14, Stefano Calza wrote:
> 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
>
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-- 
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fhcrc.org
Phone: (206) 667-3158