
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 <mailinglist.honeypot@gmail.com>
To: Chu Zhang <chuzhang@ymail.com>
Cc: bioc-sig-sequencing@r-project.org
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 <chuzhang@ymail.com> 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


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