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

Hervé Pagès hpages at fhcrc.org
Sun Mar 30 20:12:42 CEST 2014

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


> Best,
> Liang

Hervé Pagès

Program in Computational Biology
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