Exactly. Jennifer's solution for outputting unmapped reads involves splitting the FASTQ file into basically two FASTA files, one with sequences and the other with the corresponding quality score string. So, yes, they would be matched files.

On Wed, Jul 31, 2013 at 4:42 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Wednesday, July 31, 2013, Mayank Tandon wrote:

That's a neat trick, and I definitely wouldn't have thought of that approach, so thanks for that!

After I finished writing this out, I realized it was super long. So here are the questions I'm asking up front, so you can choose whether or not to read the details. Thanks!

1. How do I output the quality scores when converting from FASTQ to FASTA?

You can't, unless you mean converting a FASTQ file into a FASTA and matching QUAL file?

Peter