Tophat Installation

Question

[KS]

hello

I am trying to install TopHat on my windows 7 system and I am trying to follow the steps given http://tophat.cbcb.umd.edu/tutorial.html and I am lost in this process. Could any one guide me in stalling TopHat on windows system.

Is TopHat fusion algorithm installed on Galaxy Server?

[User 59]

A bit more information would be helpful. How are you trying to install it? Via Cygwin?

[carol091188]

I'm trying via Cygwin, but I never did it, could you tell me where can I find more information about install it?

[WouterDeCoster]

While not what you are looking for, you should know that Tophat 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. (If you can't get access to that publication, let me know and I'll -cough- help you.) There are also alternatives such as STAR followed by htseqcounts or featureCounts and DESeq2 or edgeR...

Answer 1

[JC]

Tophat runs in Linux or Mac OS X systems, not Windows.

Tophat 2 now includes fusion detection. Just wait until the Galaxy servers update their version (if you can wait).