Hello all. I ll try and be clear this time around about what i am asking. I am trying to run cuffdiff. Before i ran tophat2, got the accepted hits then sorted them and then put them into cuffdiff. my command line is this :

cuffdiff -o /Users/.../cuffdiffmefrep1-rep2/ -L mef1,mef2 -p 2 ~/.../mm9genes.gtf /Users/....sortedmef1accepted.bam /Users/..../sortedmef2accepted.bam

but i get 0kb output files. Any solution there?

Also i tried htseq-count. my command line is :

htseq-count -f bam -o samtout -q /Users/..../sortedes1accepted.bam /Users/j.../mm9genes.gtf

but i cant seem to get the ouput files. Only print out in terminal. Do i have to put also -i and -t ? and how to do that?

I use mac os