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
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