I want to run Cuffdiff on my Tophat alignment files.
I have 6 samples : 3 conditions (A,B,C) with 2 replicates each . I'd like to compare each condition between each other (A vs B, A vs C, B vs C)
cuffdiff -L c1,c2,hs1,hs2,rv1,rv2 \ -p 32 ../Araport11_GFF3_genes_transposons.201606_filtred.gff \ -o cuffdiff/ \ SRR2033948/accepted_hits.bam,SRR2033949/accepted_hits.bam,SRR2033950/accepted_hits.bam,\ SRR2033951/accepted_hits.bam,SRR2033952/accepted_hits.bam,SRR2033953/accepted_hits.bam
But that doesn't return me what I want