How to fix mates in PE Illumina data after alignment and discard reads with no mates?

Question

[lakhujanivijay]

How to fix mates in PE Illumina data after alignment and discard reads with no mates?

[Brian Bushnell]

It's better to do that before alignment. Indeed, it is best to use data that is not corrupted. So the real question is, how did you manage to destroy the pairing of the reads during preprocessing? You need to redo the preprocessing with a pair-aware tool.

Answer 1

[memory_donk]

I'm sure there are bigger-name pieces of software that will do it, but these scripts by the MacDonald lab are pretty quick and easy and have good instructions. You need Picard installed to use them but they're written in Perl

http://www.mcdonaldlab.biology.gatech.edu/bioinformatics.htm

edit: no affiliation, I just found them very useful when I was getting started.