BWA interpretation

[Inma]

Hi all,

I have seen in BWA that several reads stop together in the same base. Do you know why it happens?

You can see like a "wall" where the sequencing can't go on and only a few reads cross this "wall".

My genome is a bacterial genome.

Thank you very much,

Inma

[rbagnall]

Hi Inma,

I too have seen this. BWA can trim reads with low quality, and if there is a difficult-to-sequence region, such as a homopolymer run, then many reads will have low quality at that position and get trimmed.

I think that is what may cause the 'wall' effect.

Either that, or you have not removed duplicate reads?

[swbarnes2]

I doubt the problem is bwa. I bet if you aligned with bowtie, you'd see the same thing.

There are a lot of possibilities. Maybe your reference isn't right. Or maybe your library really looks like that. There are probably certain areas of the genome that fragment poorly.

Are you doing any quality trimming of the reads?