# \#closed-reference **URL:** https://forum.qiime2.org/tag/closed-reference/100.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [bivalve gut microbiota, water and soil samples What OTU cluster?](https://forum.qiime2.org/t/bivalve-gut-microbiota-water-and-soil-samples-what-otu-cluster/33894)
**Author:** [@Katerina\_Fialova](https://forum.qiime2.org/u/Katerina_Fialova)\ **Replies:** 11\ **Last updated:** [January 19, 2026, 5:05pm UTC](https://forum.qiime2.org/t/bivalve-gut-microbiota-water-and-soil-samples-what-otu-cluster/33894 "2026-01-19T17:05:10Z")
Hi, my name is Kejty, and I am still a newbie in the world of bioinformatics. I am studying gut microbiota from bivalves, along with water and soil microbiomes. My samples were sequenced on Illumina, targeting the V3–V4… --- ## [Closed reference OTU picking of V3-V4 amplicon against full-length reference database](https://forum.qiime2.org/t/closed-reference-otu-picking-of-v3-v4-amplicon-against-full-length-reference-database/32808)
**Author:** [@SEOK](https://forum.qiime2.org/u/SEOK)\ **Replies:** 3\ **Last updated:** [March 21, 2025, 3:51pm UTC](https://forum.qiime2.org/t/closed-reference-otu-picking-of-v3-v4-amplicon-against-full-length-reference-database/32808 "2025-03-21T15:51:33Z")
Hello, everyone ! I have sequencing data with two different 16S rRNA regions with V3-V4 and V1-V9 (full-length HiFi reads) and want to minimize the effect of different regions. After denoising each sequencing data (V3-V… --- ## [closed reference OTU picking steps](https://forum.qiime2.org/t/closed-reference-otu-picking-steps/21952)
**Author:** [@dong316](https://forum.qiime2.org/u/dong316)\ **Replies:** 2\ **Last updated:** [January 22, 2022, 11:08pm UTC](https://forum.qiime2.org/t/closed-reference-otu-picking-steps/21952 "2022-01-22T23:08:20Z")
Hi. I am going to do a meta-analysis which combines V4, V3-4, V3-5, and unknown regions. So I decide to do closed reference OTU picking using q2-vsearch. Here are my questions: Is denoising and clustering are totally s… --- ## [Trouble in alignment and taxonomy assignment for dataset with big dataset](https://forum.qiime2.org/t/trouble-in-alignment-and-taxonomy-assignment-for-dataset-with-big-dataset/19483)
**Author:** [@kartika](https://forum.qiime2.org/u/kartika)\ **Replies:** 3\ **Last updated:** [May 17, 2021, 3:23pm UTC](https://forum.qiime2.org/t/trouble-in-alignment-and-taxonomy-assignment-for-dataset-with-big-dataset/19483 "2021-05-17T15:23:18Z")
Hi, i am quite new for this analysis. I am running analysis of microbiota for gastric biopsy samples of 250 patients. I already tried to use the workflow suggested in the Moving Picture tutorial (dada2, denoise etc) u… --- ## [Is it necessary to set p-perc-identity the same to the level of reference sequences in vsearch cluster-features-closed-reference](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)
**Author:** [@HeinzG](https://forum.qiime2.org/u/HeinzG)\ **Replies:** 2\ **Last updated:** [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 "2021-01-20T07:45:55Z")
Hello, I plan to use qiime vsearch cluster-features-closed-reference to pick up OTUs using the green\_99otus.qza as reference sequences, but I am wondering if it is necessary for me to set --p-perc-identity to 0.99. Coul… --- ## [Closed Reference OTU picking vs taxonomic annotation](https://forum.qiime2.org/t/closed-reference-otu-picking-vs-taxonomic-annotation/13457)
**Author:** [@osman](https://forum.qiime2.org/u/osman)\ **Replies:** 2\ **Last updated:** [February 4, 2020, 12:38pm UTC](https://forum.qiime2.org/t/closed-reference-otu-picking-vs-taxonomic-annotation/13457 "2020-02-04T12:38:13Z")
Hi, I have no background in these analysis but I would like to clearify my mind in the following. During OTU clustering, one of the methods is Closed reference. How is it different than reqular taxonomic annotation oth… --- ## [How to set p-perc-identity with UNITE dynamic reference sequences?](https://forum.qiime2.org/t/how-to-set-p-perc-identity-with-unite-dynamic-reference-sequences/12240)
**Author:** [@Andrew\_Richards](https://forum.qiime2.org/u/Andrew_Richards)\ **Replies:** 2\ **Last updated:** [October 30, 2019, 10:32pm UTC](https://forum.qiime2.org/t/how-to-set-p-perc-identity-with-unite-dynamic-reference-sequences/12240 "2019-10-30T22:32:57Z")
Hey, I am trying to use qiime vsearch cluster-features-closed-reference command for ghost tree and I am wondering how I should set --p-perc-identity if I am using a unite dynamic reference sequences since dynamic uses e… --- ## [vsearch clustering and feature classifiers](https://forum.qiime2.org/t/vsearch-clustering-and-feature-classifiers/11675)
**Author:** [@the\_dummy](https://forum.qiime2.org/u/the_dummy)\ **Replies:** 2\ **Last updated:** [September 27, 2019, 6:47am UTC](https://forum.qiime2.org/t/vsearch-clustering-and-feature-classifiers/11675 "2019-09-27T06:47:01Z")
Hello, I'm a bit confused about how to use vsearch clustering and feature classifiers. Can I use the table generated by open or closed reference to draw taxa bar plots? Is it reliable to do that way? Or should I skip cl… --- ## [Help with greengenes gg\_13\_8 reference otus](https://forum.qiime2.org/t/help-with-greengenes-gg-13-8-reference-otus/10567)
**Author:** [@Olumide](https://forum.qiime2.org/u/Olumide)\ **Replies:** 1\ **Last updated:** [July 8, 2019, 2:08pm UTC](https://forum.qiime2.org/t/help-with-greengenes-gg-13-8-reference-otus/10567 "2019-07-08T14:08:13Z")
I am trying to download the greengenes reference otus via this link ftp://greengenes.microbio.me/greengenes\_release/gg\_13\_5/gg\_13\_8\_otus.tar.gz but it seems not to be working. Please how do I resolve this? --- ## [Fix required: Tips in a tree detected as repeated](https://forum.qiime2.org/t/fix-required-tips-in-a-tree-detected-as-repeated/10184)
**Author:** [@rodrigogarlop](https://forum.qiime2.org/u/rodrigogarlop)\ **Replies:** 4\ **Last updated:** [June 25, 2019, 6:11pm UTC](https://forum.qiime2.org/t/fix-required-tips-in-a-tree-detected-as-repeated/10184 "2019-06-25T18:11:23Z")
Hi I have been using QIIME 1 for a while now and I'm finally switching to QIIME2 out (v 2019.1). I was trying to compare Q1 and Q2 OTUs with ASVs but I'm having some problems when running Sepp for the phylogenies constr… --- ## [Vsearch closed-reference clustering terminated automatically when running](https://forum.qiime2.org/t/vsearch-closed-reference-clustering-terminated-automatically-when-running/9789)
**Author:** [@Lea](https://forum.qiime2.org/u/Lea)\ **Replies:** 3\ **Last updated:** [May 19, 2019, 10:19pm UTC](https://forum.qiime2.org/t/vsearch-closed-reference-clustering-terminated-automatically-when-running/9789 "2019-05-19T22:19:34Z")
Hi, I am new to QIIME and QIIME2. I met a problem when running the vsearch closed-reference clustering with the Greengene 97\_otus.qza as reference. The task seems could run normally at the beginning, but it just got term… --- ## [PICRUSt and Qiime2](https://forum.qiime2.org/t/picrust-and-qiime2/4957)
**Author:** [@ellen](https://forum.qiime2.org/u/ellen)\ **Replies:** 2\ **Last updated:** [July 11, 2018, 4:09pm UTC](https://forum.qiime2.org/t/picrust-and-qiime2/4957 "2018-07-11T16:09:05Z")
Hello, I am trying to make a .biom file suitable for use in PICRUSt; however, I can not find reference sequences (would be apart of the --i-reference-sequences command in the qiime vsearch cluster-features-closed-refere… --- ## [Vsearch cluster-features-closed-reference error](https://forum.qiime2.org/t/vsearch-cluster-features-closed-reference-error/3200)
**Author:** [@Paraqui](https://forum.qiime2.org/u/Paraqui)\ **Replies:** 2\ **Last updated:** [February 28, 2018, 12:26pm UTC](https://forum.qiime2.org/t/vsearch-cluster-features-closed-reference-error/3200 "2018-02-28T12:26:12Z")
I ran this trying to generate a closed reference file which I would then use to generate a BIOM file for analysis by PICRUSt and I received the following error qiime vsearch cluster-features-closed-reference \\ --i-tab… --- ## [‘reference\_sequences’ is not a subtype of FeatureData\[Sequence\]](https://forum.qiime2.org/t/reference-sequences-is-not-a-subtype-of-featuredata-sequence/2979)
**Author:** [@Guido\_Lopes\_dos\_Sant](https://forum.qiime2.org/u/Guido_Lopes_dos_Sant)\ **Replies:** 2\ **Last updated:** [February 23, 2018, 4:37pm UTC](https://forum.qiime2.org/t/reference-sequences-is-not-a-subtype-of-featuredata-sequence/2979 "2018-02-23T16:37:04Z")
Dear Greg, Thank you for this tutorial. I have performed this tutorial with my own data (demultiplexed, quality-controlled sequence data). So I followed option 1 and went on to perform closed-reference clustering. Howe… --- ## [Closed-Reference clustered-table with all reference OTUs](https://forum.qiime2.org/t/closed-reference-clustered-table-with-all-reference-otus/2955)
**Author:** [@msap](https://forum.qiime2.org/u/msap)\ **Replies:** 1\ **Last updated:** [February 9, 2018, 2:43pm UTC](https://forum.qiime2.org/t/closed-reference-clustered-table-with-all-reference-otus/2955 "2018-02-09T14:43:44Z")
Howdy! I've clustered some sequences from a study (not mine) to the GreenGenes 99% OTU database using cluster-features-closed-reference. However, the resulting clustered table only shows the frequency of GG OTUs that hav… --- ## [Qiime2 issue: Going from deblur to closed ref](https://forum.qiime2.org/t/qiime2-issue-going-from-deblur-to-closed-ref/2650)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 14\ **Last updated:** [January 23, 2018, 2:16am UTC](https://forum.qiime2.org/t/qiime2-issue-going-from-deblur-to-closed-ref/2650 "2018-01-23T02:16:45Z")
I'm trying to run a deblur command and then use the delburred sequences to run a closed reference command. The command I run is: qiime vsearch cluster-features-closed-reference \\ --i-table table-deblur.qza --i-sequ… --- ## [Picrust support?](https://forum.qiime2.org/t/picrust-support/1376)
**Author:** [@hongwei2017](https://forum.qiime2.org/u/hongwei2017)\ **Replies:** 22\ **Last updated:** [December 14, 2017, 9:59am UTC](https://forum.qiime2.org/t/picrust-support/1376 "2017-12-14T09:59:18Z")
Dear QIIME Team Does qiime2 support using PICRUST? I may need generating files for Picrust analysis. But don't know if qiime2 can exporting pertinent files for this. thanks! --- ## [Tax bar plots of CR-clustered vs. feature-classified data](https://forum.qiime2.org/t/tax-bar-plots-of-cr-clustered-vs-feature-classified-data/2081)
**Author:** [@steff1088](https://forum.qiime2.org/u/steff1088)\ **Replies:** 1\ **Last updated:** [December 4, 2017, 5:45pm UTC](https://forum.qiime2.org/t/tax-bar-plots-of-cr-clustered-vs-feature-classified-data/2081 "2017-12-04T17:45:56Z")
Hi everybody, there was this question that came up in a separate discussion: If I can use the closed reference clustering to obtain abundances for a taxa barplot, what do I need a classifier for? cheers, steffen