Question

Tophat software installation

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7.7 years ago

saj98 ▴ 140

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

software error • 10k views

ADD COMMENT • link updated 7.7 years ago by h.mon 35k • written 7.7 years ago by saj98 ▴ 140

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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 Tuxedo suite has been superseded by this combo.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.

ADD REPLY • link 7.7 years ago by GenoMax 148k

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

ADD REPLY • link 7.7 years ago by saj98 ▴ 140

score 0 · Answer 1 · 2017-04-19

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7.7 years ago

h.mon 35k

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.

ADD COMMENT • link 7.7 years ago by h.mon 35k

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

ADD REPLY • link 7.7 years ago by h.mon 35k