Thank you, your response helps me so much.
what is the minimum No. reads/sample after deblur?
I heard people tend to target 20000reads/sample, is it the number for sequencing raw reads or the reads after quality control? I have 12000 reads after deblur for one sample. Is it still OK to keep it while rarefaction (>12000)? I have triplicate samples per sample type, other samples have 17000-30000 reads after deblur. majority of them have >20000reads/sample