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