[Bio-bwa-help] bwa - writing unaligned reads to a separate file

[Neel A. <na...@wh...>]

Hello,

Is there any way to write/save unaligned reads to a file. I have large 
number of reads that are not aligned to the reference genome. If I can 
write them into a file either in fasta or any other format, I can use 
that file to see what those reads are.

Thank you,

Neel