On Thu, Jul 28, 2011 at 9:43 PM, Assaf Gordon <gor...@cshl.edu> wrote:
> Hi,
> The attached patch enables the BWA wrapper to work with Illumina-1.3+ FASTQ 
> files without Grooming (which goes well with the name of the tool: "Map with 
> BWA for Illumina" ).
> Actually,
> Changing the XML and the python code, testing the tool and mapping to the 
> mouse genome all together took less time than grooming one 4.2GB FASTQ file :)
> Comments are welcomed,
>  -gordon

Hi Gordon,

You asked for comments, so:

It concerns me that you're doing this for both "fastqillumina" format
(good) and "fastqsolexa" (bad). Treating the later as fastqillumina
would give negative scores and probably cause trouble. Unless BWA
copes but if so it is a poor choice of argument name?

In the XML wrapper you've not updated the help text for the
FASTQ parameters to indicate it would now accept Illumina
FASTQ as well as Sanger FASTQ.


P.S. It is a patch file, but it has extension xml??

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