Given two conditions (control and treated) with 4 replicates. How can I get genes with FPKM for each replicate?
Control Replicates: C1, C2, C3, C4
Treated Replicate: T1, T2, T3, T4
For example, for a gene TP53 I need the following
TP53 FPKM(c1), FPKM(c2),FPKM(c3),FPKM(c4), FPKM(t1),FPKM(t2),FPKM(t3),FPKM(t4)
I tried the following command
cuffdiff -o diff_out -b genome.fa -p 8 -L CR,TR -u merged_asm/merged.gtf CR_R1_thout/accepted_hits.bam,CR_R2_thout/accepted_hits.bam,CR_R3_thout/accepted_hits.bam,CR_R4_thout/accepted_hits.bam TR_R1_thout/accepted_hits.bam,TR_R2_thout/accepted_hits.bam,TR_R3_thout/accepted_hits.bam,TR_R4_thout/accepted_hits.bam
But, I got combined FPKM for two conditions not for replicates
How can I get FPKM for each replicates?