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:[email protected]] Sent: Tuesday, July 07, 2009 4:13 PM To: Wu, Xiwei Cc: [email protected] 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 > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:30}} > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
