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Old 11-12-2013, 11:37 AM   #1
Location: Boston

Join Date: Nov 2013
Posts: 13
Default Cufflinks novel gene discovery

I have two questions regarding novel gene discovery using Cufflinks:

1.) Does anyone have a good answer for what the appropriate FPKM cutoff value should be during gene discovery using Cufflinks. I have approximately 13,000 "novel genes" identified using Cufflinks, but many of them possess very low FPKMs. What should be the appropriate FPKM that a gene should possess in order to be accepted as a true novel gene? Is there a consensus? I was thinking of using an FPKM of 5 but was unsure if this was too high.

2.) I have run 4 insect stages of RNA-seq data (all with coverage of approximately 140-200 million reads) through Cufflinks and Cuffcompare. It indicates that there are no novel genes that are present in more than 1 of the time point according to the file [name].tracking Am I misinterpreting the results?

Thanks everyone!
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