BWA wrapper with Illumina-1.3+ FASTQ files
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
On Thu, Jul 28, 2011 at 9:43 PM, Assaf Gordon <gordon@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. Peter P.S. It is a patch file, but it has extension xml??
Hello Peter and all, Peter Cock wrote, On 07/28/2011 05:08 PM:
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.
Peter
P.S. It is a patch file, but it has extension xml??
These are all valid comments, here's an updated patch (with a ".patch" extension :) ). Thanks! -gordon
Hi Assaf, I placed the patch into a ticket for us to be able to track status more easily: https://bitbucket.org/galaxy/galaxy-central/issue/635/patch-bwa-wrapper-with... Thank you! Jen Galaxy team On 7/28/11 2:26 PM, Assaf Gordon wrote:
Hello Peter and all,
Peter Cock wrote, On 07/28/2011 05:08 PM:
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.
Peter
P.S. It is a patch file, but it has extension xml??
These are all valid comments, here's an updated patch (with a ".patch" extension :) ).
Thanks! -gordon
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
participants (3)
-
Assaf Gordon -
Jennifer Jackson -
Peter Cock