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-accept-fastq
 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.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
> 
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> 


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