gravatar for debitboro

2 hours ago by


Dear all,

I run the following cuffmerge command,

cuffmerge -o COMPARE -g /path/to/reference.gtf -s /path/to/reference.fa transcripts.txt

but I got the following error.

Error: gtf_to_sam not found on this system. Did you forget to include it in your PATH?

I googled the error and most of the people that encountered that error said it should be fixed by simply adding the cufflinks path to the PATH variable.

I've added the cufflinks path to my PATH variable as follows, but I'm still getting the same error.

export PATH=$PATH:/usr/local/src/cufflinks-2.2.1

More strangely, when I entered just gtf_to_sam command in the prompt, I got the following which seems the gtf_to_sam command works perfectly!!!

Need help, I don't know how to fix the issue

Thanks in advance

Source link