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Old 01-09-2014, 12:12 PM   #4
Location: Boston

Join Date: Nov 2013
Posts: 13

Using upwards of 600 million reads, I have aligned the reads to the reference genome using the Tuxedo suite of programs and using a RABT assembly. This gives me around 10,000 completely unknown genes that aren't associated with any isoforms or known genes. I want to say, with confidence, that the FPKM associated with an unknown gene represents the gene having full coverage and being fully represented.

The problem I'm having is that I cannot determine a good way to create this cutoff point, any ideas?
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