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.


Which Galaxy instance are you using, and when was it last updated?

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