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

[Peter Rice]

Peter C. wrote:

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

EMBOSS does that with all sequence formats. The case of the original
sequence is preserved and reproduced on output. We have not specified
upper or lower case only for any of our current output formats.

We provide command line options to force sequences to be converted to
upper or lower case if the user want to specify one or the other -
usually just to convert sequences for post processing by some other tool.

regards,

Peter Rice