8 Dec
2011
8 Dec
'11
5:53 a.m.
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