Question: Stringtie error message
0
gravatar for saj98
3 months ago by
saj9850
saj9850 wrote:

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

software error • 249 views
ADD COMMENTlink modified 5 weeks ago by Biostar ♦♦ 20 • written 3 months ago by saj9850
1
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.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by h.mon10k

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?

ADD REPLYlink written 3 months ago by Ram13k

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

ADD REPLYlink written 3 months ago by WouterDeCoster25k
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