What you are seeing are either 1) you don't have enough sequencing depth to resolve expression of lowly expressed genes or 2) there are actually that many genes that just aren't being expressed. How many reads do you have for the sample?
I would generate a rarification plot of increasing subsets of your reads vs number of genes with tags more than X reads. For example, a plot where you take 1,2,3,4,... million reads and see how many genes have more than 10 reads mapping for each increasing subset.
If you see a plateau, then you probably do have enough read coverage and what you are seeing is probably a biological effect. If no plateau, then you might not have enough read depth.
I might have read your question incorrectly. Are you saying 50% of the genes in your sample have FPKM of 0 or one specific gene has FPKM of 0 in 50% of your samples?
modified 5.7 years ago
5.7 years ago by
Damian Kao ♦ 15k