Stringtie not find the merged gtf reference

Question

[schlogl]

Hi there I am trying to use stringtie to count reads using the merged gtf from bam files but the command that I find it to do the job give me back an error.

$ stringtie –e –B -p 8 -G genome/TAIR10/annotation/stringtie_merged.gtf -o ballgown/Athaliana_root_1/Athaliana_root_1.gtf sam_bam/Athaliana_root_1.bam

Error: input file –e cannot be found!

I try to copy the merged file to different directories but not seems to work! I got this command from a tutorial. Do you have any clue or suggestion why this isn't working?
Thanks

[lieven.sterck]

Stupid suggestion but have you looked in the manual/help section of the stringtie software? ;)

it seems like the first argument it expects is a file and not a parameter or other option. (== try to restructure you cmdline)

[schlogl]

I am trying that...maybe my question is dumb, but when you put out a tutorial, well maybe you get it right. 8)

https://bioinformatics.uconn.edu/rnaseq-arabidopsis/

[lieven.sterck]

indeed it is mentioned like this in this tutorial.

So either it's just wrong or it might be a version difference?

Answer 1

[ATpoint]

The syntax is wrong. From the manual: stringtie <aligned_reads.bam> [options]*

It means the input file is the first argument after stringtie which currently is -e, which is why the tool interpretes it as input.

Must be:

stringtie sam_bam/Athaliana_root_1.bam –e –B -p 8 -G genome/TAIR10/annotation/stringtie_merged.gtf -o ballgown/Athaliana_root_1/Athaliana_root_1.gtf

[schlogl]

Thanks ATpoint, generally I check the manual... but you right

stringtie <aligned_reads.bam> [options]*

Answer 2

[schlogl]

I got it done...

$ stringtie -e -B -p 4 sam_bam/Athaliana_root_1.bam -G genome/TAIR10/annotation/stringtie_merged.gtf -o ballgown/Athaliana_root_2/athaliana_root_1.count -A ballgown/Athaliana_root_1/Athaliana_root_1.out

Thanks

[lieven.sterck]

Following ATpoint instructions this should/will not work , as the input bam is still not the first argument after the stringtie cmd.