Hi
I want to find high and low express genes from cufflinks output for one RNA sample. How can I choose an FPKM cut-off to judge whether the corresponding genes is expressed or not? could anyone provides me some detailed about it?
Thanks in advance
1 answer
Hi hana, I think this is the same as your question in a slightly broader context How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?. In the strict sense the answer must be, you can't detect genes that are not expressed, because each time the expression could be just below your detection limit. You can only detect genes that significantly above a threshold to be transcribed, and whatever threshold has to be arbitrary. That was at least the conclusion of the previous question.
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Michael Dondrup
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