I included a negative control sample when I was extracting gDNA where I added no sample (just the DNA extraction reagents with nuclease-free water) to control for the contamination. I got back my 16S sequencing data and analyzed my samples. My negative control sample has a very low read number, 114 reads, to be exact. I know this is expected because there is no sample input.
My question is when filtering Feature Table, how low can you go? I usually set 1500 reads, but my negative control sample will be removed, and I'm not sure if I can go as low as 100 reads. Can I assume, at this point, my negative control sample contains no significant contamination? Any thought is appreciated! Here are the sequence reads of my samples:
Sample ID Feature Count