Stringtie error message

Question

[saj98]

Hello everyone

I am using the following command which already explained in the nature protocol paper

stringtie –e –B -p 8 -G stringtie_merged.gtf -o ballgown/WS021/WS021.gtf Bam/WS021.bam

The issue it gave me the following error

Error: input file –e cannot be found!

However, when I delete -e and -B options, it run fine. Can anyone explain for me the problem? I appreciate your time and help

[h.mon]

stringtie –e –B -p 8 -G stringtie_merged.gtf -o ballgown/WS021/WS021.gtf Bam/WS021.bam

Has the above command line been copy / pasted from your scripts? Note that –e and –B (with dash) are different from -e and -B (with hyphen), and command line parameters are indicated by hyphens, not dashes.

[Ram]

This looks like a positional parameters/named parameters error. Maybe the program is not equipped to handle -e in the position you're passing it in?

[WouterDeCoster]

Try putting the -e and -B at the end of the command, maybe.