hi all,
I run cuffdiff 1.3.0 on Normal (6 replicates) vs Tumor (10 replicates). The command is:
cuffdff -p 20 -o . -b hg19.fa genes.gtf -L Normal,Tumor n1.bam,n2.bam,..,n6.bam t1.bam,t2.bam,..,t10.bam
This is my first time to run cuffdiff on data with replicates, hoping to get the DE results as well as the FPKM of each gene in EACH SAMPLE. Unfortunately, from the "genes.fpkm_tracking" file, I only get one FPKM value for each GROUP rather than each SAMPLE. I wonder if I missed something?
Thanks.
I run cuffdiff 1.3.0 on Normal (6 replicates) vs Tumor (10 replicates). The command is:
cuffdff -p 20 -o . -b hg19.fa genes.gtf -L Normal,Tumor n1.bam,n2.bam,..,n6.bam t1.bam,t2.bam,..,t10.bam
This is my first time to run cuffdiff on data with replicates, hoping to get the DE results as well as the FPKM of each gene in EACH SAMPLE. Unfortunately, from the "genes.fpkm_tracking" file, I only get one FPKM value for each GROUP rather than each SAMPLE. I wonder if I missed something?
Thanks.
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