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

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


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