I am trying to use the job script;
cuffdiff -p 10 -L Egg,Metacercaria PRJEBWB9PAULAnnotations.gff3 EggB1/tophat_out/accepted_hits.bam,EggB2/tophat_out/accepted_hits.bam MetB1/tophat_out/accepted_hits.bam,MetB2/tophat_out/accepted_hits.bam,MetB3/tophat_out/accepted_hits.bam
However, I get the error;
Error: cuffdiff requires at least 2 SAM files
/EggB1/tophat_out/accepted_hits.bam,/EggB2/tophat_out/accepted_hits.bam: No such file or directory
I have checked the paths to these files and everything appears to be as it should for my script to work.