Where in cuffdiff we can specify that the bam files are associated to different conditions?
cuffdiff -o outputname -b genome.fasta -p <cores> -L C1, C2 -u merged.gtf C1R1/accepted_hits.bam C2R1/accepted_hits.bam C1R1/accepted_hits.bam C2R2/accepted_hits.bam
How does this association work? does option
L needs to be specified like
Any help would be greatly appreciated.