Question: Cuffmerge: Command Not Found
0
gravatar for martinkara7
5.3 years ago by
martinkara720
martinkara720 wrote:

Hello, I am doing RNA seq anaylsis. TO prepare to do actual anaylsis i am doing the paper example http://bio.lundberg.gu.se/courses/vt13/nprot.2012.016.pdf So to solve any issues that may come up. An issue came up, cuffmerge. I installed the latest version cufflinks on my linux and doubled checked all correct. I ran the command on the command line

 cuffmerge -g genes.gtf -s genome.fa assemblies.txt

And got the error

cuffmerge: command not found

I ran it in the same directory been using to get this far but now ...

Please can anyone suggest what might be wrong

cufflinks cuffmerge rna-seq • 3.6k views
ADD COMMENTlink modified 5.3 years ago by Istvan Albert ♦♦ 80k • written 5.3 years ago by martinkara720
0
gravatar for Istvan Albert
5.3 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

as the error says, cuffmerge was not found.

Please read more on how to run programs from the command line.

http://www.linuxquestions.org/questions/linux-newbie-8/how-to-run-program-from-command-line-313900/

ADD COMMENTlink written 5.3 years ago by Istvan Albert ♦♦ 80k

Got it, thanks. ITs a python script.

ADD REPLYlink written 5.3 years ago by martinkara720
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