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?

Thanks,

Raj

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