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Old 01-10-2014, 06:19 AM   #5
rboettcher
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Location: Berlin

Join Date: Oct 2010
Posts: 71
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Novel depends on which reference annotation you are using. If there is more than one source, start with filtering out everything that shows any overlap with any known gene. Next, you can filter for genes with >1 exons, as Cufflinks reports a lot of FP exons and spliced transcripts can be easier validated in the lab. Besides that, there is no general rule concerning a cut-off for FPKM values. In fact, there is still some discussion ongoing whether FPKM is actually a good representation of expression in general, so I would argue to just look at the FPKM distribution and then chose a cut-off deemed OK.

Best,
René
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