[BioC] readGappedAlignmentPairs with multimapping reads

[Martin Morgan]

On 06/02/2012 06:08 AM, Vedran Franke [guest] wrote:
>
> How does the readGappedAlignmentPairs from the GenomicRanges library handle reads that map to several places in the genome?
>
> Sometimes it can happen that one pair of the read is flagged as properly paired even if the other read maps to several locations, how is this handled?

The full details will eventually be documented on 
?readBamGappedAlignmentPairs and ?makeGappedAlignmentPairs; the author 
is currently taking a few days off. My understanding is that each 
alignment is a separate record, and that in the SAM specification one 
mate tells the location of the second mate (and vice versa) so that 
pairs can be identified unambiguously (except when the mate alignments 
differ only in the pattern of indels within an end).

More details will be forthcoming.

Martin

> Thank you in advance!
>
>   -- output of sessionInfo():
>
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>   [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>   [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>   [7] LC_PAPER=C                     LC_NAME=C
>   [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.8.3 IRanges_1.14.2      BiocGenerics_0.2.0
> [4] plyr_1.6            stringr_0.6         BiocInstaller_1.4.4
>
> loaded via a namespace (and not attached):
> [1] stats4_2.15.0 tools_2.15.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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