# OTU abundance threshold - 0,005% of what
**URL:** https://forum.qiime2.org/t/otu-abundance-threshold-0-005-of-what/15775
**Category:** General Discussion
**Created:** [July 20, 2020, 8:06am UTC](https://forum.qiime2.org/t/otu-abundance-threshold-0-005-of-what/15775 "2020-07-20T08:06:20Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@Ruben](https://forum.qiime2.org/u/Ruben)
#### Post date: [July 20, 2020, 8:06am UTC](https://forum.qiime2.org/t/otu-abundance-threshold-0-005-of-what/15775/1 "2020-07-20T08:06:20Z")
Hi,
I´m trying to understand how the secondary filtration of OTUs in Qiime is working. The 2013 paper on quality filtering recommends removing OTUs containing less than 0,005% reads: "For datasets where a mock community is not included for calibration, we recommend the conservative threshold of (c = 0.005%)."
My question: Is it 0.005% out of all reads in the whole sequencing run, or 0.005% out of all reads in one of the samples in the sequencing run?
Regards,
Ruben Dyrhovden
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### Author:  [@ChrisKeefe](https://forum.qiime2.org/u/ChrisKeefe)
#### Post date: [July 20, 2020, 10:23pm UTC](https://forum.qiime2.org/t/otu-abundance-threshold-0-005-of-what/15775/2 "2020-07-20T22:23:00Z")
Hi @Ruben!
A point of process first: I've moved your question to General Discussion, as it seems to be a question about best practices discussed in the literature, rather than a software support issue. If I'm misinterpreting your question, please feel free to clarify and/or move back into the correct category.
I'm not a bioiniformatics expert, and am uncertain which 2013 paper you're referencing. If you can clarify which paper, the community might be better able to answer your question.
Finally, if this _is_ a software question, we should be clear on whether you're using QIIME (which is no longer supported), or QIIME 2, which replaced QIIME in early 2018. The two tools work very differently.
Best,
Chris
🐑
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### Author:  [@Ruben](https://forum.qiime2.org/u/Ruben)
#### Post date: [July 21, 2020, 6:52am UTC](https://forum.qiime2.org/t/otu-abundance-threshold-0-005-of-what/15775/3 "2020-07-21T06:52:53Z")
Hi,
thanks for your reply. I will try to make my question clearer.
The paper I am referring is titled " Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing" by Bokulich et.al.: [Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing | Nature Methods](https://www.nature.com/articles/nmeth.2276)
My question is about what is defined as "secondary filtering / OTU abundance threshold (c)" in the cited paper.
I understand from reading other posts on the forum that OTU-abundance threshold filtering is no longer recommended if using deblur/dada2 [Filter Feature Table - #3 by cla](https://forum.qiime2.org/t/filter-feature-table/4416/3) .
Although not recommended any longer in QIIME2 I would really appreciate if you could help me understanding the 0,005% OTU abundance filtering approach, as it is used in a lot of microbiome studies. I have not been able to understand clearly if it is 0,005% of all reads in the entire sequencing run, or 0,005% of all reads in one sample.
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### Author:  [@ChrisKeefe](https://forum.qiime2.org/u/ChrisKeefe)
#### Post date: [July 22, 2020, 1:37am UTC](https://forum.qiime2.org/t/otu-abundance-threshold-0-005-of-what/15775/6 "2020-07-22T01:37:30Z")
@Ruben, according to Dr. Bokulich himself, it's 0.005% of all reads in the _entire sequencing run_.
Have fun out there!
🐩
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [August 22, 2020, 7:37am UTC](https://forum.qiime2.org/t/otu-abundance-threshold-0-005-of-what/15775/7 "2020-08-22T07:37:35Z")
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