E: Package 'tophat' has no installation candidate

Question

[athira112athira]

Hi, I try to install "Tophat" on my laptop (ubuntu 20.04), But it shows an error message. I need suggestions to fix this, it's really helpful if somebody can add their knowledge.

athira@Athira:~$ sudo apt-get install tophat
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package tophat is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'tophat' has no installation candidate

[brunobsouzaa]

As everyone said, it's not recommended to use Tophat anymore. I would suggest you using STAR.

[Bastien Hervé]

Try to update your APT databases

sudo apt-get update
sudo apt-get upgrade

If it does not work you can always try with the binary : Tophat software installation

[athira112athira]

Thank you all for your valuable suggestions.

Answer 1

[colindaven]

Please do not use outdated methods like Tophat, there's even a whole article about it:

https://www.the-scientist.com/news-opinion/scientists-continue-to-use-outdated-methods-30438

Alternatives: STAR, Hisat2.

Answer 2

[i.sudbery]

Tophat has not been packaged on the Ubunutu package archives since ubuntu 18.04 because it is deprecated and no longer supported.

There are still good reasons to download and install tophat (or tophat2) - particularly if you want to exactly replicate an old study, or use it in a benchmarking study (although of course it might be an unfair comparison compared to more modern aligners).

If you do still wish to install (and i'd recommend against, for the reasons colindaven outlines, unless for replication purposes), follow the instructions on the tophat website: https://ccb.jhu.edu/software/tophat/tutorial.shtml#inst