how to install cuffmerge on my ubunto 06.4

Question

[hamid_fiuji]

how can i install cuffmerge on my ubunto 16.4.my cufflinks need not to be installed since it is immage of an installed program and i just use this command ./cufflinks but when i ma using cuffmerge i get errors. how can i run that? thanks

[WouterDeCoster]

Someone mentions cufflinks? Time for my recurrent comment!

You should know that the old 'Tuxedo' pipeline of Tophat(2) and 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, or pseudo-alignment using salmon.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[hamid_fiuji]

i am sorry my ubunto version is 16.04

[GenoMax]

Edit your original post to add new information or use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

[GenoMax]

i ma using cuffmerge i get errors

Please be specific about what error you got. It looks like you don't need to install the program since it already appears to be on your machine.

[Arup Ghosh]

Once you have installed cufflinks, there is no need to install cuffmerge separately. Please, the error details.