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DON'T USE TOPHAT - LIOR PACHTER TWEET
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Hello <uname>,

You should know that the old 'Tuxedo' pipeline of Tophat(2) and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: [Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown][1].  There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.


  [1]: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html


https://twitter.com/lpachter/status/937055346987712512