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?
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anonymous5982 •
Oh okay thank you for clarifying! Is there a big reason why STAR or hisat2 outperforms Tophat?
(from one of the authors of the original TopHat; and read the paper linked to in that tweet).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
Thank you so much that is really helpful!
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