On Nov 20, 2012, at 11:21 AM, Kevin Y wrote:

> Hello,
> 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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