On Sat, Jun 2, 2012 at 11:48 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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.
>
>
I think I can add a few details, since I've been playing with this lately.

I think the intent at least is to drop the read pairs that are not
one-to-one. I'm a little skeptical that it's actually working correctly
though, because it seems to always drop exactly one read pair from my BAMs,
even though there must be more than one that is ambiguous.

Take this with a grain of salt though.

Michael


> 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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>
>
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