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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/