[Biopython] comparing bam files

[Peter Cock]

On Tue, Sep 20, 2011 at 10:46 PM, Abhishek Pratap
<abhishek.vit at gmail.com> wrote:
> Thanks for the reply Peter. I know my requirement sure does confusing but
> this is something we need to do in order to extract the reads which are
> stranded. In our case we want the reads where read 1 maps to same strand and
> read 2 on the other strand and eliminate the cases where read 2 falls on the
> same strand and read 1 on the opposite strand.

Do you have something backwards, or perhaps I should go to sleep now...
it sounds like you are talking about paired reads here (read 1 and read 2).

It would be normal for Sanger (capillary) or Illumina paired end (or Illumina
mate pairs) reads to map to opposite strands.

Technically Roche paired end reads would map to the same strand (due
to the way they sequence over the boundary of a circularised fragment)
but I'm not 100% sure if any read aligners/assemblers reflect this. I know
that sff_extract and MIRA flip one of the Roche 454 reads so that they
act like classical Sanger or Illumina paired ends.

> I am looking into pysam to see if it can help me . Does pysam have another
> mailing list  or this is the right forum to ask pysam related questions ? I
> am sure I will have some as soon as I begin poking into it.
> -Abhi

There are a few people on the Biopython lists who do use pysam, and
might be able to help, but pysam has a separate mailing list.

Peter