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tophat software running issues

Tophat 2.1.1 software not are not ./configure --prefix=/path/to/tophat_base_dir \ --with-boost=/path/to/boost_prefix_dir while building of tophat, please anybody face the same problem, do it for needful. Thank you.

rna-seq software error next-gen
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updated by lieven.sterck lieven.sterck • written by ajitdake26693 • ajitdake26693

Hello ajitdake26693,

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. There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

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

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written by lieven.sterck lieven.sterck

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