Minimum number of reads/data needed in a sample for successful data analysis with QIIME2

[colinbrislawn (Colin J Brislawn)]

Hello Tammy,

Welcome to the forums!

These are some great questions and I can answer a few of them.

@tamardigrade

Is there a minimum number of reads/output data in a sample file needed in order to successfully process your samples, and does this change between ASV/DADA versus clustering?

Technically no, but more is better. Initial studies in this field had a few hundred. Now, I would hope for thousands of reads per sample at least!

@tamardigrade

Is there a way to estimate between file size (as seen on WinSCP) and number of reads?

Not really, because this depends on both the size and complexity of the reads. But there's a better way. After downloading and decompressing the file, you can directly count the number of reads in each file. Qiime does this after import.

@tamardigrade

More broadly, how do folks use negative controls for their sample analysis? As a lower limit threshold, or as a way to judge 'background noise' and subtract this out of all the other samples (or see if its present in other samples.) Or how else?

This is my favorite question and by far the hardest. I use negative controls to establish 'background noise' as you mention, but what to do next is an open question.