On Thu, Feb 10, 2011 at 6:42 PM, Peter wrote:
> On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor wrote:
>>
>> Sounds like this should be added into the main release. It would save a lot
>> of time/disk space instead of using Groomer.
>>
>
> I agree. Maybe Dan can take care of it - I don't have bowtie setup
> on our local Galaxy (yet) so I wouldn't be able to test the proposed
> fix.
>
> In the long term however the Solexa/Illumina FASTQ formats are on
> their way out since CASAVA 1.8 will switch to the Sanger FASTQ
> encoding: http://seqanswers.com/forums/showthread.php?t=8895
>

Hi Stephen,

Maybe you should file an issue on bitbucket about extending the Bowtie
wrapper to support fastqillumina as well as fastqsanger as input?
https://bitbucket.org/galaxy/galaxy-central/issues?status=new&status=open

The current version of the wrapper is here if you want to look at it:
https://bitbucket.org/galaxy/galaxy-central/src/default/tools/sr_mapping/bowtie_wrapper.xml

Peter
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