Tophat vs HISAT

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Question: Tophat vs HISAT

18 months ago by

Beatriz Ramos • 10

Beatriz Ramos • 10 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 • 2.4k views

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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by Beatriz Ramos • 10

18 months ago by

Anton Nekrutenko ♦ 1.7k

Penn State

Anton Nekrutenko ♦ 1.7k 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 (https://galaxyproject.org/tutorials/rb_rnaseq/#read-mapping) explains how HiSat2 works.

ADD COMMENT • link modified 18 months ago • written 18 months ago by Anton Nekrutenko ♦ 1.7k

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