# Is it necessary to set p-perc-identity the same to the level of reference sequences in vsearch cluster-features-closed-reference

**URL:** https://forum.qiime2.org/t/is-it-necessary-to-set-p-perc-identity-the-same-to-the-level-of-reference-sequences-in-vsearch-cluster-features-closed-reference/18143
**Category:** User Support
**Tags:** closed-reference
**Created:** [January 19, 2021, 2:14pm UTC](https://forum.qiime2.org/t/is-it-necessary-to-set-p-perc-identity-the-same-to-the-level-of-reference-sequences-in-vsearch-cluster-features-closed-reference/18143 "2021-01-19T14:14:03Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![HeinzG](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/h/58f4c7/32.png) [@HeinzG](https://forum.qiime2.org/u/HeinzG)
#### Post date: [January 19, 2021, 2:14pm UTC](https://forum.qiime2.org/t/is-it-necessary-to-set-p-perc-identity-the-same-to-the-level-of-reference-sequences-in-vsearch-cluster-features-closed-reference/18143/1 "2021-01-19T14:14:03Z")

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Hello,

I plan to use qiime vsearch cluster-features-closed-reference to pick up OTUs using the green\_ **99** _otus.qza as reference sequences, but I am wondering if it is necessary for me to set --p-perc-identity to **0.99**. Could I just set --p-perc-identity to **0.97 or 0.90** when I use green_ **99** \_otus.qza as reference sequences. Just like below:

qiime vsearch cluster-features-closed-reference   
--i-table table.qza   
--i-sequences rep-seqs.qza   
--i-reference-sequences green\_99\_otus.qza   
--p-perc-identity 0.97 \ #or 0.90  
--p-strand "both"   
--o-clustered-table table-cr-green-99.qza   
--o-clustered-sequences rep-seqs-cr-green-99.qza   
--o-unmatched-sequences unmatched-cr-green-99.qza \

Thanks for your time!

Heinz

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### Author: ![jwdebelius](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jwdebelius/32/9655_2.png) [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [January 19, 2021, 4:36pm UTC](https://forum.qiime2.org/t/is-it-necessary-to-set-p-perc-identity-the-same-to-the-level-of-reference-sequences-in-vsearch-cluster-features-closed-reference/18143/2 "2021-01-19T16:36:00Z")

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Hi @HeinzG,

It is not necessary! Large databases do clustering to reduce the database size - thus the 97% or 99% identitiy. You can cluster against they at any identity you choose. However, I think it's recommended to match the two.

Best,  
Justine

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### Author: ![HeinzG](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/h/58f4c7/32.png) [@HeinzG](https://forum.qiime2.org/u/HeinzG)
#### Post date: [January 20, 2021, 7:45am UTC](https://forum.qiime2.org/t/is-it-necessary-to-set-p-perc-identity-the-same-to-the-level-of-reference-sequences-in-vsearch-cluster-features-closed-reference/18143/3 "2021-01-20T07:45:55Z")

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Thank you for your help!

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [February 20, 2021, 1:46pm UTC](https://forum.qiime2.org/t/is-it-necessary-to-set-p-perc-identity-the-same-to-the-level-of-reference-sequences-in-vsearch-cluster-features-closed-reference/18143/4 "2021-02-20T13:46:00Z")

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