minimum freqeuncy threshold

dada2-stats-summ.qzv (1.2 MB)
featuretable.qzv (622.8 KB)
Hello, I am working with paired-end reads for human microbiota V3-V4 region. I ran my samples through cutadapt and filtered the sequences. However, I am not sure whether my minimum frequency is acceptable or is too high in order to proceed with downstream analyses. In general is there any range for how much my minimum frequency should be?

Hello Rakaya,

Welcome to the forums! :qiime2:

Having >70% of reads pass filter is ok.
Having >64% of reads merge is also good, because that's almost all of them that passed the filter.

More reads are better because that gives you more resolution to detect changes between samples.

You could do a power analysis to learn more, but 30k reads per sample is better than a lot of early studies in this field.

You are off to a good start! Let us know if you have any other questions along the way.