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.


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

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.


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