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Old 05-04-2016, 11:35 AM   #1
Location: Ithaca

Join Date: Jan 2009
Posts: 26
Default problem about StringTie expression

The StringTie could output expression on both gene-level (with -A parameter) and transcript-level (t_data.ctab).
The total FPKM value of gene is ~1,000,000; but the total FPKM value of transcript is just ~600,000.
For the same sample and reference GTF, the total FPKM of transcript is ~2,400,000 using cufflinks to compute the expression.

The expression show big difference between Cufflinks and StringTie. Which one is correct?
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