Dear All researchers,
The sequence count in various samples is very, each sample is replicate, there are five replicates, The sequence count is like 100, 200, 600, 1000, 1100, 1200, 2200,3500, 4000, 5500, 6000, 7000, 8900, 9000, 10000, 10500, What would be the sampling depth for alpha and beta core metrics phylogenetic analysis? I have three replicates 100, 200, 600 falls below 1000, For example, 100 and 200 are the two replicates of a sample, similarly, 600 is a replicate of another sample. If I use a sampling depth of 1000, of course, I will miss all the 100, 200 and 600, In this way, I miss two replicates 100 and 200 of one sample and one replicate of another sample. Would it affect my diversity? What is your suggestion? I am very confused, If I use 200 or 100 as a threshold, I could not get a good rarefaction curves, My samples are from the a land which is watered by rainfall.
Waiting for your suggestions