More bug fixes, and a paired-end TopHat tool. Available here: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_2011_04_04.tar.bz2
See the interface here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1 Comments are very welcomed, Cufflinks is next, -gordon Assaf Gordon wrote, On 03/30/2011 09:21 AM: > Still very much work-in-progress, but I'd like to hear any comments or ideas > that you might have. > > No need to install, just visit here to see TopHat's interface: > http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_se1 > > Main differences from the existing TopHat tool: > 1. Far fewer visible options > 2. Select "Existing gene mode" (use GTF file) or do De-novo junction > detection (or both) > 3. Allow insertions/deletions detection (with the latest tophat). > 4. Allow user to specify custom command line parameters. > 5. Accepts Fasta, FastqSanger, FastqIllumina (but not generic "fastq", per > your feedback). > > If you think there are other critical and often used options, let me know. > > updated code is available here: > http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_tools_1.tar.bz2 > > -gordon > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
