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Old 12-04-2017, 08:57 AM   #4
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,825

It is not that it can't be used. It is more that you should not be using TopHat pipeline for any new data. TopHat is in maintenance mode and even its developers recommend that you use HISAT2, their latest creation.

You may need to try a newer aligner (e.g. BBMap, STAR, HISAT2) and see what works best for your data.
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