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Old 06-05-2012, 11:29 AM   #1
Location: USA

Join Date: Aug 2010
Posts: 94
Default cuffdiff: tracking FPKM of a gene in EACH sample

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?

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Old 06-05-2012, 07:17 PM   #2
Location: USA

Join Date: Aug 2010
Posts: 94

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!
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Old 05-26-2015, 09:45 AM   #3
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Default Hello

Got it from another post:
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