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

[Dan Bolser]

2009/8/5 Peter <biopython at maubp.freeserve.co.uk>:
> 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?

Agree.


> Peter
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