Tophat software installation

Question

[saj98]

Hello I would like to install tophat software on ubuntu, Does anybody have an idea which command I have to use? I appreciate your help

[GenoMax]

If you are just starting please use HISAT2/Stringtie (or any other splice-aware aligner) instead of TopHat. Tuxedo suite has been superseded by this combo. See this paper for a detailed protocol.

[saj98]

I am trying to use it, hopefully I can get it.

Answer 1

[h.mon]

You may install from Ubuntu repo:

sudo apt-get install tophat

Or you may download the binary and install it:

wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
tar -xvzf tophat-2.1.1.Linux_x86_64.tar.gz
mv tophat-2.1.1.Linux_x86_64/ ~/bin/tophat-2.1.1/

And to use it:

export PATH=~/bin/tophat-2.1.1:$PATH

P.S.: do not forget to install bowtie2 if you install the downloaded binary.

[h.mon]

You may also install from source, but this is an unnecessary complication.