Samples missing from DADA2 table but not denosing stats

[Nicholas_Bokulich]

Hi @saatkinson,

@saatkinson

The 5 missing samples are: ES1-1-B_10-10-17_8, ES1-1-B_12-08-17_67, ES1-1-D_04-06-18_186, ES1-3-A_09-29-17_-3, ES1-3-D_02-02-18_123

It looks like those 5 samples are the only 5 that have 0 reads post-filtering:

I think the feature table must be made after denoising, dropping all samples that have 0 sequences, and then chimera removal happens after that — @benjjneb is that correct?

@saatkinson

I know the sequences aren’t the best, with a lot that have low sequence counts/non-chimeric output.

Those 5 samples (and many others) cannot be revived any way you slice it, since the input read counts are so low. However, you are losing many reads at the filtering step, which leads me to believe you might be able to save more reads in your other samples by adjusting your trimming/truncation parameters. Let us know if you have any questions about that.

Good luck!