On Nov 20, 2012, at 11:21 AM, Kevin Y wrote:
> Is there a way to get unmapped reads from tophat?
Only the very latest tophat version 1.4.1 IIRC (and maybe tophat2 from the
beginning) save unmapped reads into a fastq.gz file output,
and its not an option.
I don't think the galaxy output puts this into your history yet.
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