On Thu, Dec 8, 2011 at 6:02 AM, Praveen Raj Somarajan wrote: > > All, > > I'm wondering why do we need to convert Illumina FASTQ into sanger > using FastQ Groomer before mapping with BWA in galaxy. The lastest > version of BWA itself added -I option to use Illumina data directly. What's > your opinion on this? > > Secondly, I found that "Map with BWA for Illumina" uses -I option in > the commandline during execution, even for sanger formatted reads. > How does it impact the results?
As the name suggested, original that wrapper assumed Illumina FASTQ encoding. This was fixed in August 2011 using a patch from Assaf Gordon, see Issue 635. https://bitbucket.org/galaxy/galaxy-central/issue/635 Which Galaxy instance are you using, and when was it last updated? Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/