On 09/02/2011 19:09, Dannon Baker wrote:
On Feb 9, 2011, at 12:47 PM, Stephen Taylor wrote:
Thanks.
What if (after upload) this is your first step? With 'Upload' you don't get the
option to do 'Change Datatype'.
I'm not exactly sure I follow. If the first step in your workflow after the
Input Dataset step is Bowtie, then you won't want to do this in the workflow,
it should happen prior to that. The workflow expects that you're supplying the
correct format for that first step.
When you are first uploading the file you can specify at that time that it
should be a fastqsanger file. For datasets that are already in a history, you
can click the pencil icon on the history item and change the datatype there
without running the fastq groomer.
Let me know if I've misunderstood and this doesn't cover what you're looking to
do.
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.
Thanks for you help,
Steve
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