in an RNA-seq experiment, what threshold would you use to define a set of expressed or active genes in a cell line?
I am trying to define a set of expressed (active) genes in my cell line for some downstream analysis. What would be your approach for defining this subset of active genes from an RNA-seq experiments? is there a minimum fpkm you would use? some standard deviation from normalized expression?
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This has been asked many times before. Please google for 'fpkm cutoff biostars', 'expressed cutoff biostars' or similar queries. With some effort you find posts spanning the last 10 years.
Try: https://bioinformatics.stackexchange.com/questions/687/what-methods-are-available-to-find-a-cutoff-value-for-non-expressed-genes-in-rna/ for a start.