Problems with Mock community -- Quality control

[doudou2047 (孟琼)]

Hi, Good day.

I put 4 kinds of the control.

1. only 1 bacteria (genome)
2. 20 Bac genomic materia from ATCC (https://www.atcc.org/products/all/MSA-1002.aspx#documentation)
3. 20 Bac genomic materia from Zymo Research.
   (https://files.zymoresearch.com/protocols/_d6305_d6306_zymobiomics_microbial_community_dna_standard.pdf)
4. Negtive control

The pipline is based on the moving picture tutorial with DADA2.
And the results I attached like that.
The negtive control could see the false postive species.
And 2 mock community are 20 bac genomic materia evenly mixed.
Could you please let me know how to do the quality control and make the other samples adjusted with the control?
Thank you so much.
Best,
QIong

[Nicholas_Bokulich]

@doudou2047

The negtive control could see the false postive species.

Many of these will be cross-contamination, not background contamination (e.g., from the lab or reagents). There are a few discussions on this forum about how to handle negative controls and cross-contaminants, use the search function to find these discussions.

@doudou2047

Could you please let me know how to do the quality control and make the other samples adjusted with the control?

Find the discussions I mentioned — this is a problematic area and there are not great solutions out there. One thing I can advise is to not just remove features found in the negative controls. QIIME 2 does not have any methods to "make the other samples adjusted with the control", nor do any perfect methods exist out there, but you may want to check out decontam (and R package, not part of QIIME 2), which attempts to identify reagent contaminants based on the negative control.

Good luck!