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.


The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  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:

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

Reply via email to