a sample with low reads

General Discussion
1

Hi everyone,

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
N-4 116520
2XP-2 110204
2XP-3 105989
N-1 103517
N-5 101636
N-3 96620
N-2 88587
2XP-4 87894
2XP-1 84129
4XP-2 83158
4XP-3 79276
4XP-4 77263
4XP-1 69524
SmartControl 6097
Ctrl-ve 114

Thank you,
Abdul

2

Hello!
I guess that you already got all the information that you needed from the negative control - there is almost nothing (great!). You can remove it from the analysis and proceed without it.

Best,

3 Likes
3

Thanks al ot! I just needed some kind of confirmation.