Hi,
I am in the process of mapping my reads to the genome using Tophat in galaxy. However, I see that the Tophat tool has been deprecated in the galaxy platform. Can I still use it to perform my analysis or should I use HISAT2?
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Hi @NIKITA_JHAVERI,
Tophat developers recommend using HISAT2 (developed by the same group), as they state that it is more accurate and much more efficient.
Regards
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Alternatively you can also use Star 
to map your reads!
Happy research!
Bjoern
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