[Open-bio-l] Mixed case sequence strings in FASTQ?

[Peter]

Hi all,

Another FASTQ issue to debate: Should we care what case the sequence
strings are? I've never seen anything written down, but all the
examples I recall used upper case. But there is nothing to stop people
using mixed case, is there?

With FASTA on the other hand, while all uppercase is most common,
mixed case has its uses (e.g. representing trimmed regions, or low
quality scores).

I would suggest that OBF tools all treat the sequence in FASTQ files
as is, and preserve the case on output.

Any thoughts?

Peter