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

[Peter]

On Mon, Aug 10, 2009 at 2:02 PM, Peter Rice<pmr at ebi.ac.uk> wrote:
> 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.

Cool. It looks like we are on the same wavelength here :)

Peter