Question: Tophat vs HISAT
gravatar for Beatriz Ramos
17 months ago by
Beatriz Ramos10 wrote:

Hi, I've been using Tophat to align RNA-seq reads followed by Cufflinks to estimate FPKM. Now that Tophat is out of the tools list, what is the main difference between using Tophat and HISAT?

rna-seq tophat cufflinks • 2.3k views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 17 months ago by Beatriz Ramos10
gravatar for Anton Nekrutenko
17 months ago by
Penn State
Anton Nekrutenko1.7k wrote:

HiSat (in particular HiSat2 that is currently on Galaxy) is the next generation of spliced aligner from the same group that have developed TopHat. It is MUCH faster and you can use its output for your old pipeline as well. This tutorial ( explains how HiSat2 works.

ADD COMMENTlink modified 17 months ago • written 17 months ago by Anton Nekrutenko1.7k
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