Aligning Paired End Reads With Bwa: Has Anybody Learnt Some Valuable Lessons To Share With Others?

Question

[Steffi]

I just wonder if one has some valuable advice regarding how to align paired end data - e.g. regarding number of allowed suboptimal alignments.

I would be interested in parameter settings (e.g. if any special choice turned out as especially useful and for what reason) or any traps one might easily fall into when continuing the preprocessing.

Actually, I did not come across any specific problem, I am just curious about other peoples experiences.

[Sean Davis]

Are you asking about a parameter setting for BWA or something about the types of alignments you get back?

Answer 1

[Swbarnes2]

I think it's going to depend a lot on your project, and your data set. If you are working in an organism where your best reference sequence isn't very accurate, or close to your sample, you might want to relax the paramters. If you have a poor quality run, you might want to relax the parameters. I don't think you can generalize.