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Question: Tophat Settings
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gravatar for Jack Colicchio
6.8 years ago by
Jack Colicchio • 10
Jack Colicchio • 10 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
rna-seq tophat • 760 views
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modified 6.8 years ago by Jeremy Goecks • 2.2k • written 6.8 years ago by Jack Colicchio • 10
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gravatar for Jeremy Goecks
6.8 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
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.
ADD COMMENT • link written 6.8 years ago by Jeremy Goecks • 2.2k
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