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Old 09-03-2012, 07:49 AM   #5
Junior Member
Location: beijing

Join Date: Apr 2012
Posts: 9
Default use cufflinks or cuffdiff to get the gene expression value?

I used tophat cufflinks and cuffdiff to analysis my mRNA sequencing data, I am confused about the gene expression value. We have 7 samples in my expreiment, I can used cufflinks to produce every gene's expression value(FPKM) in each stage , and I can also used cuffdiff to get the gene's expression value by running cuffdiff with 7 samples together. But the gene's expression value produced by cufflinks and cuffdiff is not the same, so could you give me a instruction about that. Thank you.
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