On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor <stephen.tay...@imm.ox.ac.uk> wrote: > On 10/02/2011 13:05, Peter Cock wrote: >> >> On Thu, Feb 10, 2011 at 12:49 PM, Stephen Taylor >> <stephen.tay...@imm.ox.ac.uk> wrote: >>> >>> I think you have but it doesn't help. :-) >>> >>> The issue is we get a lot of Illumina 1.3+ format FASTQ files and bowtie >>> in >>> Galaxy by default doesn't accept them although there is an option on the >>> command line bowtie to read these. So I think the solution seems to be >>> either hardwire the code in our local Galaxy instance to use the >>> --solexa1.3-quals option or (probably more useful) put a drop down list >>> in the web UI to allow the user to set the format of the fastq sequences >>> on the bowtie tool. >>> >> >> Not the best approach. >> >> I think you should update the XML to include the --solexa1.3-quals option >> if the Galaxy file format is fastqillumina, see for example (in the >> reverse situation) the -Q 33 option is only used on fastqsanger when >> calling the FASTX tools, e.g. >> >> >> https://bitbucket.org/galaxy/galaxy-central/src/default/tools/fastx_toolkit/fastx_clipper.xml >> >> That way the user must mark their FASTQ file type as usual (at upload time >> or via the "pencil icon" to edit the attributes), and then bowtie will be >> called appropriately. >> > > Ok. Cool. I didn't realise you could do that! > > 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 Peter _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
