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Old 02-16-2016, 08:44 AM   #2
Senior Member
Location: Vancouver, BC

Join Date: Mar 2010
Posts: 275

I would try gffcompare (by the same author) instead of "stringtie --merge" because it seems to be more stringent. I have also experienced the same issue that you report, but it is worse for a large genome. In my case, "stringtie --merge" generated 3X more transcripts than the reference, while gffcompare only generated about 2X more. You can also discard novel loci with gffcompare if you want to only consider the reference set.

Alternatively, you can increase the thresholds for stringtie to merge transcripts.
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