6.2 years ago
Kansas City, MO
Would it be possible to do this with Picard? Specifically, Picard's IlluminaBasecallsToSam
Picard - IlluminaBasecallsToSam
Then, if needed, using _ SamToFastq_ also from Picard.
If you have the entire basecalls directory, this might be worth checking out. I don't see a lot of documentation... a potentially relevant SEQAnswers question is unaddressed:
SEQAnswers question on IlluminaBasecallsToSam