Question

Is Tophat 2 good?

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2.1 years ago

anonymous5982 ▴ 10

Hello, I am analysing a paper which used genome guided assembly with RNA-Seq data to assemble the transcriptome of some RNA. They used Tophat2 v.2.1.1 to do the assembly with the --b2-very-sensitive option. I have seen work which says that tophat is not great but I am a novice and don't really understand why.

Could someone please explain to me the limitations of using Tophat2?

Tophat RNA-Seq • 847 views

ADD COMMENT • link updated 2.1 years ago by Ram 43k • written 2.1 years ago by anonymous5982 ▴ 10

score 1 · Answer 1 · 2022-04-06

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2.1 years ago

ATpoint 82k

The tophat tools are not assemblers but aligners, and both Tophat1 and 2 are deprecated (for years now). You should be using something recent, like STAR or hisat2 unless a legacy burden forces you not to.

ADD COMMENT • link 2.1 years ago by ATpoint 82k

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Oh okay thank you for clarifying! Is there a big reason why STAR or hisat2 outperforms Tophat?

ADD REPLY • link 2.1 years ago by anonymous5982 ▴ 10

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The reason not to use it is performance. "TopHat2 is consistently among the worst performers on both human and malaria T2 and T3 libraries." https://t.co/deW5dgYc29 There are many other published benchmarks corroborating this result.
— Lior Pachter (@lpachter) April 24, 2019

(from one of the authors of the original TopHat; and read the paper linked to in that tweet).

ADD REPLY • link 2.1 years ago by dsull ★ 6.0k

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Thank you so much that is really helpful!

ADD REPLY • link 2.1 years ago by anonymous5982 ▴ 10

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Hi, why did you delete the post?

ADD REPLY • link 2.1 years ago by Ram 43k

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I would start by reading the papers to learn about performance comparisons.

ADD REPLY • link 2.1 years ago by ATpoint 82k