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. best, ido ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
