Mapping E.coli PE reads

[aggp11]

Hi,

I have to align PE reads from the E.coli DH10B sequencing. I am thinking of using BWA sampe. Could E.coli being a circular genome cause any alignment issues? If yes, then I don't see an option to for aln/sampe that could handle this. So is anybody aware of doing PE E.coli data alignment using BWA? Also, are there any better alignment tools for E.coli PE data?

Any help regarding this would be appreciated.

Thanks,
Praful

[maubp]

Could E.coli being a circular genome cause any alignment issues?

Yes, because BWA won't map any reads over the origin, and could potentially reject paired reads spanning the origin.

[swbarnes2]

You will have some reads that cross from the "end" of your genome to the origin of your genome, and those won't map. And you will have reads where one read is at the "end", and the other is after the origin, and these will be marked as improperly paired.

But it's not going to make much difference in the grand scheme of things.

[aggp11]

Thanks a lot for your prompt replies. This makes sense and this is what I thought might happen, but just wasn't sure. So based on this, I would assume BWA aln/sampe should still work for most of the reads and I'll just have a slightly bigger number of improperly paired reads.

Thanks again guys.
Praful