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/bow... Peter