I figured it out. Please disregard my last email. Thanks, Ilya From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, July 11, 2011 10:00 AM To: galaxy-dev(a)lists.bx.psu.edu; galaxy-user-bounces(a)lists.bx.psu.edu Subject: [galaxy-dev] TopHat V1.1 with GTF files I was wondering how to pass a GTF file to the current Tophat implementation in Galaxy. It says that -G/--GTF is an implemented parameter but that option does not show up. BTW, what version of tophat is supplied with the most recent stable release. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny@illumina.com<mailto:ichorny@illumina.com> 858-202-4582