On Tue, Mar 29, 2011 at 4:46 PM, Assaf Gordon <gor...@cshl.edu> wrote:
> Hi Dan,
>
> Daniel Blankenberg wrote, On 03/29/2011 10:55 AM:
>> When files are added to Galaxy, the datatype can be directly set to
>> any of the fastq variants (e.g. fastqillumina), which removes the
>> requirement of grooming (but should only be done when users know what
>> they are doing).
>
> I'm not using the "get data" tool, we have our own import tools (uploading
> huge files with HTTP is not stable enough for me). You're right that I should
> change the format of this tool from 'fastq' to 'fastqillumina' (but the tool
> pre-dated all those built-in formats in galaxy, so I never bothered to update
> it...).

Why not do the Illumina to Sanger conversion as part of your pipeline
that gets the data into Galaxy (and mark the files as fastqsanger)?
As Glen said, with a C tool that isn't really so slow. That future proofs
you for the pending Illumina CASAVA 1.8 release, and means you don't
need to maintain divergent Bowtie wrappers for Galaxy.

Peter
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