cufflinks error on ubuntu 16.04

Question

[sa1987]

hi

I am working in ubuntu 16.04

i wanted to install cufflinks 2.2.1

but i get error saying

Reading package lists... Done Building dependency tree
Reading state information... Done Package cufflinks 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 'cufflinks' has no installation candidate

but other software like bowtie,velvet etc can be installed ....

cufflinks cuffdiff cannot be installed and shows error

plz help ...

Answer 1

[WouterDeCoster]

Please specify what you tried, it's helpful to show the command you used.

Have you seen this page? Installing cufflinks

In addition, you should know that Tophat/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. (If you can't get access to that publication, let me know and I'll -cough- help you.) There are also other alternatives, including alignment with STAR and bbmap,...

[sa1987]

hi

command used was sudo apt-get install cufflinks error Reading package lists... Done Building dependency tree Reading state information... Done Package cufflinks 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

i tired troubleshooting in many ways but no use..

thank you for the information and i can access the publication.... i m new to RNA seq analysis...i m trying it out

........ i have installation problem for stringtie also

[WouterDeCoster]

Then read the installation instructions. Not all software is installed using apt-get.