Hi Stephen and Peter, This change is definitely possible, and because the SAM format specifies that its quality scores are phred scaled and ASCII offset of 33 (regardless of provided input) it shouldn't cause complications downstream. We'll add this to our todo list. I created a ticket: https://bitbucket.org/galaxy/galaxy-central/issue/471/allow-bowtie-mapper-to... that you can follow if you like. Thanks, Dan On Feb 10, 2011, at 1:42 PM, Peter Cock wrote:
On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor <stephen.taylor@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.taylor@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/...
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
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