Question: Stringtie error message
0
gravatar for saj98
12 months ago by
saj9880
saj9880 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 • 581 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 12 months ago by saj9880
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 10 months ago • written 10 months ago by h.mon20k

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 12 months ago by RamRS18k

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

ADD REPLYlink written 12 months ago by WouterDeCoster32k
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