Cuffmerge: Command Not Found

Question

[martinkara7]

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

[Pierre Lindenbaum]

http://www.cyberciti.biz/faq/linux-unix-command-not-found-error-and-how-to-get-rid-of-it/

Answer 1

[Istvan Albert]

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/

[martinkara7]

Got it, thanks. ITs a python script.