cuffdiff: tracking FPKM of a gene in EACH sample

[mrfox]

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.

[mrfox]

24 people have viewed this but no one answers ? :-)
I believe it is a common operation to track the FPKM of each gene in each sample. How do you guys to that?

Thank you!

[fernisoites]

Hello

Got it from another post:

http://seqanswers.com/forums/showthread.php?t=39833