Also if your alignments are in BAM format , so can use Rsamtools to extract that region. Inspection of the cigar will tell you which reads aligned perfectly. That would be an extremely fast calculation.
Cheers Paul -----Original Message----- From: Steve Lianoglou <[email protected]> To: Chu Zhang <[email protected]> Cc: [email protected] Subject: Re: [Bioc-sig-seq] processing alignments Date: Thu, 10 Feb 2011 20:21:49 -0500 Hi, On Thu, Feb 10, 2011 at 6:48 PM, Chu Zhang <[email protected]> wrote: > Hi Guys, > > I have Bowtied (aligned) sequences against a local database having few > sequences > of length between 70-300bp. Now lets take SeqA of length 120bp from my target > database. Since the RNA-Seq reads are of length 38bp i guess, how do i > ascertain > that for instance 3 different reads aligned perfectly to cover the SeqA. I'm not sure what you mean by "aligned perfectly to cover SeqA", but -- I'd load your reads into a GRanges object which is easy to manipulate. You can look at the `coverage` function to then see how much of (and to what dept) your SeqA is covered. Be aware the "strandedness" of reads can be issue. You should be aware if your rna-seq data keeps "strand" info or not and deal with your data accordingly. Also, the I/GRange findOverlaps functionality will be your friend, too. -steve [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
