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?