I was given a genbank file (.GB) as a reference and I will be making a custom reference for cell ranger. However I need convert this genbank file to gtf. I've been looking for and trying different methods for a couple of days with no luck.
I saw this answer: How to get GTF file of virus genome but I can't seem to get Bioperl to work. I have installed it through Anaconda but when I try to load it up I receive the following error:
-bash-4.2$ perl bp_genbank2gff3.pl --dir Viral.GB --GFF_VERSION 2 perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "C.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Can't open perl script "bp_genbank2gff3.pl": No such file or directory
I'm running bioperl through linux on an HPC through ssh so I also don't have any administrative permissions.
Thank you in advance.