[BioC] A question about the function readGAlignmentPairs in GenomicRnages package

Hervé Pagès hpages at fhcrc.org
Sun Mar 30 20:51:00 CEST 2014


On 03/30/2014 11:31 AM, Niu, Liang (NIH/NIEHS) [E] wrote:
> Dear Herve,
>
> Thanks for your suggestion. I do not the paring information in the downstream analysis, therefore, readGAlignmentsList() is good.

Maybe I was not clear enough but if you don't need the pairing, then
you can just use readGAlignments(). readGAlignmentsList() will pair
everything that can be paired and this has a cost (in terms of
performance and memory usage). By using readGAlignments() you avoid
that cost and you also end up with an object that is a little bit
simpler to manipulate (i.e. a GAlignments instead of GAlignmentsList
object).

Hope that makes sense,
H.

>
> Liang
> ________________________________________
> From: Hervé Pagès [hpages at fhcrc.org]
> Sent: Sunday, March 30, 2014 2:12 PM
> To: Niu, Liang (NIH/NIEHS) [E]
> Cc: bioconductor at r-project.org
> Subject: Re: A question about the function readGAlignmentPairs in GenomicRnages package
>
> Hi Liang,
>
> Hope you don't mind that I'm cc'ing the Bioconductor mailing list, so
> other can give suggestions.
>
> On 03/30/2014 09:32 AM, Niu, Liang (NIH/NIEHS) [E] wrote:
>> Dear Mr. Pages,
>>
>> This is Liang Niu, a research fellow at the National Institute of Environmental Health Sciences.
>>
>> I am using R to read .bam files for chromatin interaction data sets. Such data sets contains alignments for  paired-end reads from ChIA-PET experiment, thus it has pairs in which two reads on different chromosomes and/or on same strand, and those pairs are valid pairs. I want to use your function readGAlignmentPairs in GenomicRnages package to read  the pairs, but the manual says that it will discard those pairs. Do you have any suggestion?
>
> You could use readGAlignmentsList() instead of readGAlignmentPairs().
> readGAlignmentsList() will keep these "discordant pairs". It will also
> keep the reads that cannot be paired.
> Note that, depending on what you will do downstream, you don't
> necessarily need to pair the reads (e.g. if you're going to compute
> the read coverage). In that case you can just load the reads with
> readGAlignments().
>
> Cheers,
> H.
>
>>
>> Best,
>> Liang
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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