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

[Chris Fields]

On Aug 10, 2009, at 8:06 AM, Peter wrote:

> 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

I believe so (sorry about lack of responsiveness, just got back in  
town).

chris