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Old 12-10-2012, 10:09 AM   #4
ajgentles
Junior Member
 
Location: Planet Earth

Join Date: Jun 2011
Posts: 4
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I found that if you tell tophat2 to generate a
transcriptome index by supplying a GTF file, but the index already
exists, it bombs out. You have to make sure not to tell it the GTF file
again.

We've basically abandoned tophat2 in favour of STAR these days.
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