[Bioc-sig-seq] read paired end alignment results

[Wu, Xiwei]

Martin,

Thanks for your fast reply. 

I am currently trying to do so as you described, by subsetting and
merging paired information using my own code. I thought I should ask
first in case it is already available.

I am thinking to calculate the coverage based on a defined window size,
mainly for copy number calculation purposes. So coverage per base is not
needed. Instead, I just need to get the number of tags aligned to a
pre-defined window. Is it possible to do so using current available
tools in BioC?

Xiwei

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Tuesday, July 07, 2009 4:13 PM
To: Wu, Xiwei
Cc: bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] read paired end alignment results

Wu, Xiwei wrote:
> Dear list,
> 
> Does readAligned function within ShortRead package support read in
> paired-end alignment result? Also, does the coverage or pileup
function
> support paired-end information? Thanks.
> 

only indirectly at the moment, e.g., by the user subletting the object
into pairs based on id or other information. There are no special
facilities in coverage or pileup to deal with this.

I'd be interested in hearing how you'd like to use this data, from you
or other users, on this list or off.

Martin


> Xiwei Wu
> Director, Microarray Service, Functional Genomics Core
> Associate Director, Bioinformatics Core
> Assistant Research Professor
> Department of Molecular Medicine
> Beckman Research Institute
> City of Hope
> 
> 
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