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Old 01-23-2014, 09:24 AM   #3
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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I have compared it to tophat, which it greatly outperforms in speed and has higher sensitivity on real RNA-seq data. I have not yet compared it to STAR - I tried to but was unable to get STAR to run without core-dumping so I gave up. I may have compiled it wrong; I'll try again eventually.

However, I don't have a really good tool for generating and evaluating synthetic RNA-seq data, so it's harder to quantify. The closest I can get is to generate synthetic DNA reads with very large deletions, which is not quite the same thing since RNA-seq data has other strange artifacts and the introns are not distributed randomly.
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