You're correct Jack. I've modified the Tophat wrapper to remove this restriction; the change will make its way to our public server soon.
Best, J. On Feb 8, 2012, at 1:27 PM, Jack Colicchio wrote: > In the new version of tophat they allow for over 3 mismatches in the initial > alignment, however your server still gives an error if you attempt to move > this over 3. This is problematic for trying to map RNAseq reads where there > is moderate divergence between the RNA and the reference genome. > > > Jack > > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
