I want run cuffdiff for two groups. each has 3 samples. Is the below code right?
cuffdiff -o diff_out -b ../genome/ce10.fa -p 2 -L em,la -u merged_asm/merged.gtf cond1.bam1,cond1.bam2,cond1.bam3 cond1.bam1,cond1.bam2,cond1.bam3
cuffdiff -o diff_out -b ../genome/ce10.fa -p 2 -L em,la -u merged_asm/merged.gtf cond1.bam1,cond1.bam2,cond1.bam3 cond1.bam1,cond1.bam2,cond1.bam3
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