# General Discussion **URL:** https://forum.qiime2.org/c/general-discussion/23.md?page=3 [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) **Page:** 4 --- ## [Exclude significant results from betadisper from adonis2?](https://forum.qiime2.org/t/exclude-significant-results-from-betadisper-from-adonis2/33469)
**Author:** [@e\_flat\_minor](https://forum.qiime2.org/u/e_flat_minor)\ **Replies:** 0\ **Last updated:** [July 19, 2025, 7:26am UTC](https://forum.qiime2.org/t/exclude-significant-results-from-betadisper-from-adonis2/33469 "2025-07-19T07:26:23Z")
Good morning, I am trying to figure out the best way to use adonis2 on my dataset. I have three distances matrices (Bray Curtis, Jaccard and weighted Unifrac). I want to test four variables (A, B, C, D). Before feeding … --- ## [16S SRNA](https://forum.qiime2.org/t/16s-srna/33536)
**Author:** [@yesiso](https://forum.qiime2.org/u/yesiso)\ **Replies:** 1\ **Last updated:** [August 2, 2025, 8:44am UTC](https://forum.qiime2.org/t/16s-srna/33536 "2025-08-02T08:44:56Z")
What I want to ask is that if I collect the 16S SRNA data from 200 samples on the NCBI website, and I have grouped the data by type, not by primer, but by process type, and now when I look at the statistics, I see that s… --- ## [Cage effect ANOVA](https://forum.qiime2.org/t/cage-effect-anova/30471)
**Author:** [@timanix](https://forum.qiime2.org/u/timanix)\ **Replies:** 11\ **Last updated:** [July 31, 2025, 4:26am UTC](https://forum.qiime2.org/t/cage-effect-anova/30471 "2025-07-31T04:26:27Z")
Dear All, I am performing the ANOVA test for the alpha diversity of some mice trials. I know that the cage effect for mice is very strong and would like to account for it in the analyses. Experimental design of the dat… --- ## [GSR database in QIIME2?](https://forum.qiime2.org/t/gsr-database-in-qiime2/33507)
**Author:** [@GustavoHdz](https://forum.qiime2.org/u/GustavoHdz)\ **Replies:** 2\ **Last updated:** [July 28, 2025, 8:19pm UTC](https://forum.qiime2.org/t/gsr-database-in-qiime2/33507 "2025-07-28T20:19:57Z")
Hello there! I am wondering if, somebody is using GSR database for phylogenetic classification? Currently I use SILVA with consistent results, but GSR (GreenGenes, Silva, RDP) database (GSR database), should be better … --- ## [Problems with Taxonomic Assignment](https://forum.qiime2.org/t/problems-with-taxonomic-assignment/33508)
**Author:** [@Amalia\_Maia](https://forum.qiime2.org/u/Amalia_Maia)\ **Replies:** 1\ **Last updated:** [July 25, 2025, 8:10pm UTC](https://forum.qiime2.org/t/problems-with-taxonomic-assignment/33508 "2025-07-25T20:10:56Z")
I am working on a microbiome project with fungal ITS data and I have generated a FASTA file containing my ASV sequences. I need to perform taxonomic classification for these ASVs. My FASTA file it contains approximately… --- ## [Why is there a size difference between my PCR product (~400 bp) and the final representative sequence (313 bp)?](https://forum.qiime2.org/t/why-is-there-a-size-difference-between-my-pcr-product-400-bp-and-the-final-representative-sequence-313-bp/33465)
**Author:** [@KYSHIM](https://forum.qiime2.org/u/KYSHIM)\ **Replies:** 4\ **Last updated:** [July 22, 2025, 6:25am UTC](https://forum.qiime2.org/t/why-is-there-a-size-difference-between-my-pcr-product-400-bp-and-the-final-representative-sequence-313-bp/33465 "2025-07-22T06:25:31Z")
Hi all, I'm using the commonly adopted COI primer pair mlCOIintF–jgHCO2198, which is designed to amplify a ~313 bp fragment. In my first-round PCR (including Illumina overhang adapters), I observed a band at around 465 … --- ## [Sequence and taxonomy files for Silva v138.2](https://forum.qiime2.org/t/sequence-and-taxonomy-files-for-silva-v138-2/33475)
**Author:** [@Laura\_R](https://forum.qiime2.org/u/Laura_R)\ **Replies:** 2\ **Last updated:** [July 21, 2025, 1:06pm UTC](https://forum.qiime2.org/t/sequence-and-taxonomy-files-for-silva-v138-2/33475 "2025-07-21T13:06:18Z")
Hello, I would like to perform taxonomic assignment on samples for which we sequenced the amplicon corresponding to the 18S ribosomal RNA gene (V4 region), using SILVA database version 138.2. However, I’m not sure wheth… --- ## [Beginner's Project](https://forum.qiime2.org/t/beginners-project/33474)
**Author:** [@balajii](https://forum.qiime2.org/u/balajii)\ **Replies:** 2\ **Last updated:** [July 21, 2025, 7:34am UTC](https://forum.qiime2.org/t/beginners-project/33474 "2025-07-21T07:34:32Z")
Hello people!! Recently I have developed interest on metagenomics and especially on QIIME 2. It has basically been my starting point to explore more about the field. I have went through moving picture tutorial which has… --- ## [Recommended Step for Merging Metagenomics Datasets](https://forum.qiime2.org/t/recommended-step-for-merging-metagenomics-datasets/33448)
**Author:** [@charlesalexandreroy](https://forum.qiime2.org/u/charlesalexandreroy)\ **Replies:** 1\ **Last updated:** [July 16, 2025, 6:37am UTC](https://forum.qiime2.org/t/recommended-step-for-merging-metagenomics-datasets/33448 "2025-07-16T06:37:29Z")
Hi all, When merging multiple datasets, I know that for 16S data, it's recommended to denoise each run separately and then merge your feature tables. I'm wondering what the recommendation is for metagenomics data? Per t… --- ## [Quality control for shotgun metagenomics](https://forum.qiime2.org/t/quality-control-for-shotgun-metagenomics/29537)
**Author:** [@maemkennedy](https://forum.qiime2.org/u/maemkennedy)\ **Replies:** 2\ **Last updated:** [March 13, 2024, 10:13pm UTC](https://forum.qiime2.org/t/quality-control-for-shotgun-metagenomics/29537 "2024-03-13T22:13:32Z")
Hi all - I am following the shotgun metagenomics workflow outlined here to analyze whole genome demultiplexed fungal data I have. I noticed the shotgun analysis information I've found (in this workflow and otherwise) doe… --- ## [Merging qiime2 sample metadata with exterior taxonomic classifications](https://forum.qiime2.org/t/merging-qiime2-sample-metadata-with-exterior-taxonomic-classifications/33431)
**Author:** [@rwhsiques](https://forum.qiime2.org/u/rwhsiques)\ **Replies:** 1\ **Last updated:** [July 13, 2025, 3:24pm UTC](https://forum.qiime2.org/t/merging-qiime2-sample-metadata-with-exterior-taxonomic-classifications/33431 "2025-07-13T15:24:14Z")
Hello! I am relatively new to bioinformatics, and qiime 2 especially, so bear with me and let me know if anything needs clarified or corrected! I am working on diet metabarcoding analyses (arthropods eaten by dragonflie… --- ## [PR2: Division vs. Phylum](https://forum.qiime2.org/t/pr2-division-vs-phylum/33426)
**Author:** [@Laura\_R](https://forum.qiime2.org/u/Laura_R)\ **Replies:** 1\ **Last updated:** [July 11, 2025, 1:36pm UTC](https://forum.qiime2.org/t/pr2-division-vs-phylum/33426 "2025-07-11T13:36:13Z")
I am using the PR2 database to assign taxonomy to my samples, and as I understand it, the “Division” rank is equivalent to the “Phylum” rank used by other databases. However, I see that the assignments at the “Subdivisio… --- ## [Is it necessary to separate ASVs classified at genus level into their respective sequences in ANCOMBC2 or other differential abundance analysis?](https://forum.qiime2.org/t/is-it-necessary-to-separate-asvs-classified-at-genus-level-into-their-respective-sequences-in-ancombc2-or-other-differential-abundance-analysis/33399)
**Author:** [@DavidRivera](https://forum.qiime2.org/u/DavidRivera)\ **Replies:** 2\ **Last updated:** [July 8, 2025, 8:53pm UTC](https://forum.qiime2.org/t/is-it-necessary-to-separate-asvs-classified-at-genus-level-into-their-respective-sequences-in-ancombc2-or-other-differential-abundance-analysis/33399 "2025-07-08T20:53:16Z")
Sequences that could only be classified at the family level or higher taxonomic ranks should be named Unclassified\_Family\_1, Unclassified\_Family\_2, Unclassified\_Family\_3, etc. so as not to lose taxonomic resolution. Full… --- ## [Transforming Alpha Diversity Metrics for Mixed Effects Modeling](https://forum.qiime2.org/t/transforming-alpha-diversity-metrics-for-mixed-effects-modeling/33401)
**Author:** [@Mahasti](https://forum.qiime2.org/u/Mahasti)\ **Replies:** 2\ **Last updated:** [July 8, 2025, 5:29pm UTC](https://forum.qiime2.org/t/transforming-alpha-diversity-metrics-for-mixed-effects-modeling/33401 "2025-07-08T17:29:08Z")
Hi Qiime 2 community! I have a question regarding transforming alpha diversity metrics for mixed effects modeling and how to present the transformed data. My study is a repeated measures design. I have analyzed four al… --- ## [Best workflow for samples with high off-target (host) amplification](https://forum.qiime2.org/t/best-workflow-for-samples-with-high-off-target-host-amplification/33362)
**Author:** [@owlpen](https://forum.qiime2.org/u/owlpen)\ **Replies:** 7\ **Last updated:** [July 8, 2025, 9:48am UTC](https://forum.qiime2.org/t/best-workflow-for-samples-with-high-off-target-host-amplification/33362 "2025-07-08T09:48:32Z")
Hi all, just wondering if anyone has experienced anything similar. At present I'm wishing I had a time machine and could go back and select a different region of 16S to target. I'm working with boar semen and the seque… --- ## [High percentage of unassigned reads (metagenomics)](https://forum.qiime2.org/t/high-percentage-of-unassigned-reads-metagenomics/33388)
**Author:** [@timanix](https://forum.qiime2.org/u/timanix)\ **Replies:** 6\ **Last updated:** [July 3, 2025, 2:30pm UTC](https://forum.qiime2.org/t/high-percentage-of-unassigned-reads-metagenomics/33388 "2025-07-03T14:30:29Z")
Hi all, I am working on the pig fecal samples that were sequenced with shotgun approach (metagenomic samples). My pipeline included: QC Host DNA removal Import to Qiime2 Taxonomy annotation with Kraken2 (moshpit) vs … --- ## [SILVA trained version for V3-V4 amplicon using 341F/785R primers](https://forum.qiime2.org/t/silva-trained-version-for-v3-v4-amplicon-using-341f-785r-primers/33385)
**Author:** [@Minely](https://forum.qiime2.org/u/Minely)\ **Replies:** 3\ **Last updated:** [July 2, 2025, 10:46pm UTC](https://forum.qiime2.org/t/silva-trained-version-for-v3-v4-amplicon-using-341f-785r-primers/33385 "2025-07-02T22:46:24Z")
Hello everyone, I’ve recently started using QIIME2 for a 16S soil microbiome analysis. After running the taxonomy classification, I noticed that I obtained a very low number of ASVs (around 1,000). Someone pointed out … --- ## [Looking for Sensible Qiime2 CLI Aliases](https://forum.qiime2.org/t/looking-for-sensible-qiime2-cli-aliases/33345)
**Author:** [@charlesalexandreroy](https://forum.qiime2.org/u/charlesalexandreroy)\ **Replies:** 1\ **Last updated:** [July 1, 2025, 7:54am UTC](https://forum.qiime2.org/t/looking-for-sensible-qiime2-cli-aliases/33345 "2025-07-01T07:54:39Z")
The tab-completion supported by Qiime + Zsh is super useful (well done to whoever implemented that!), but CLI aliases would often be faster for commands I run regularly. For example, by adding the following to my .zshrc… --- ## [How to simplify the formula gini index in QIIME2? For example write in a R script.](https://forum.qiime2.org/t/how-to-simplify-the-formula-gini-index-in-qiime2-for-example-write-in-a-r-script/31784)
**Author:** [@yangyue](https://forum.qiime2.org/u/yangyue)\ **Replies:** 2\ **Last updated:** [November 1, 2024, 8:36am UTC](https://forum.qiime2.org/t/how-to-simplify-the-formula-gini-index-in-qiime2-for-example-write-in-a-r-script/31784 "2024-11-01T08:36:37Z")
The result of Gini index on QIIME2 is puzzling！ I've used the following to calculate Gini index on QIIME2, for example: qiime diversity alpha \\ --i-table table1\_1m2-featuretable.qza \\ --p-metric gini\_index \\ --o-alpha-… --- ## [Looking for Comprehensive Qiime2 Documentation](https://forum.qiime2.org/t/looking-for-comprehensive-qiime2-documentation/33252)
**Author:** [@charlesalexandreroy](https://forum.qiime2.org/u/charlesalexandreroy)\ **Replies:** 3\ **Last updated:** [June 23, 2025, 10:32am UTC](https://forum.qiime2.org/t/looking-for-comprehensive-qiime2-documentation/33252 "2025-06-23T10:32:47Z")
Hey all, I am fairly new to Qiime2 and feel like I am struggling a bit to transition to the Qiime way of doing things. Hopefully this doesn't come across as overly whiny, but relative to other bioinformatics tools, Qiim… --- ## [Request for Pre-trained SILVA V1–V3 Naive Bayes Classifier](https://forum.qiime2.org/t/request-for-pre-trained-silva-v1-v3-naive-bayes-classifier/33314)
**Author:** [@diksha\_klair](https://forum.qiime2.org/u/diksha_klair)\ **Replies:** 2\ **Last updated:** [June 18, 2025, 7:17pm UTC](https://forum.qiime2.org/t/request-for-pre-trained-silva-v1-v3-naive-bayes-classifier/33314 "2025-06-18T19:17:55Z")
Hi QIIME2 community, I’m working on 16S rRNA amplicon sequencing using the V1–V3 region with the following primer pair: Forward: AGAGTTTGATCMTGGCTCAG Reverse: ATTACCGTGGCTGCTGG I'm using QIIME 2 version 2024.10 and w… --- ## [classify-sklearn vs classify-consensus-vsearch - classification depth](https://forum.qiime2.org/t/classify-sklearn-vs-classify-consensus-vsearch-classification-depth/33295)
**Author:** [@areaume](https://forum.qiime2.org/u/areaume)\ **Replies:** 2\ **Last updated:** [June 13, 2025, 5:01pm UTC](https://forum.qiime2.org/t/classify-sklearn-vs-classify-consensus-vsearch-classification-depth/33295 "2025-06-13T17:01:30Z")
Hi all, I ran both classify-sklearn and classify-consensus-vsearch using the PR2 database for 18S v9 samples. The result is a much lower classification depth for the classifier based method. Both methods assigned a simi… --- ## [Shotgun sequencing of Fungi - UNITE or KRAKEN2](https://forum.qiime2.org/t/shotgun-sequencing-of-fungi-unite-or-kraken2/33291)
**Author:** [@FRANCESCOMONTESI](https://forum.qiime2.org/u/FRANCESCOMONTESI)\ **Replies:** 1\ **Last updated:** [June 11, 2025, 8:29pm UTC](https://forum.qiime2.org/t/shotgun-sequencing-of-fungi-unite-or-kraken2/33291 "2025-06-11T20:29:55Z")
Hi everybody, i have fastQ files produced by shotgun DNA sequencing (paired-end) performed with illumina platform. I have sequenced 3 fungi in monocolture, so i have 3 samples, i expect 3 different species. I have 2 qu… --- ## [Feature table and representative sequences for downstream analyses](https://forum.qiime2.org/t/feature-table-and-representative-sequences-for-downstream-analyses/33297)
**Author:** [@Anandi\_Batabyal](https://forum.qiime2.org/u/Anandi_Batabyal)\ **Replies:** 1\ **Last updated:** [June 11, 2025, 8:21pm UTC](https://forum.qiime2.org/t/feature-table-and-representative-sequences-for-downstream-analyses/33297 "2025-06-11T20:21:39Z")
Hello Users, I've been using QIIME2 for some time now in my research, where I’m investigating the effects of maternal interventions in mice on the gut microbiome of their offspring. For each dam (mouse mom), I have mult… --- ## [PERMANOVA and DESeq2: Re-evaluating Covariates After Subsetting by Time Point](https://forum.qiime2.org/t/permanova-and-deseq2-re-evaluating-covariates-after-subsetting-by-time-point/33242)
**Author:** [@Naorem](https://forum.qiime2.org/u/Naorem)\ **Replies:** 1\ **Last updated:** [June 9, 2025, 6:19pm UTC](https://forum.qiime2.org/t/permanova-and-deseq2-re-evaluating-covariates-after-subsetting-by-time-point/33242 "2025-06-09T18:19:19Z")
I have approximately 200 samples with outcome labels (success or failure) and various covariates, collected across multiple time points. My analysis plan includes using PERMANOVA to identify significant covariates, follo… --- ## [maarjAM database](https://forum.qiime2.org/t/maarjam-database/33257)
**Author:** [@Salma\_Sarker](https://forum.qiime2.org/u/Salma_Sarker)\ **Replies:** 3\ **Last updated:** [June 6, 2025, 3:51pm UTC](https://forum.qiime2.org/t/maarjam-database/33257 "2025-06-06T15:51:02Z")
Hi QIIME2 community, I’m currently working on the analysis of arbuscular mycorrhizal fungi (AMF) using the 18S rRNA gene region (primers AMV4.5NF and AMDGR). I have already completed denoising with DADA2 and obtained my… --- ## [Analysing with multiple public datasets](https://forum.qiime2.org/t/analysing-with-multiple-public-datasets/33253)
**Author:** [@Shinthotrang](https://forum.qiime2.org/u/Shinthotrang)\ **Replies:** 4\ **Last updated:** [June 5, 2025, 4:49pm UTC](https://forum.qiime2.org/t/analysing-with-multiple-public-datasets/33253 "2025-06-05T16:49:19Z")
Greetings everyone! I have questions regarding analysing with multiple public datasets downloaded from SRA database. These datasets have the same target region (v3-v4), same length 600. Based on what I have read on: r… --- ## [Qiime2 ConQuR Plugin for Batch Correction (or alternative)](https://forum.qiime2.org/t/qiime2-conqur-plugin-for-batch-correction-or-alternative/33218)
**Author:** [@charlesalexandreroy](https://forum.qiime2.org/u/charlesalexandreroy)\ **Replies:** 2\ **Last updated:** [June 4, 2025, 4:04am UTC](https://forum.qiime2.org/t/qiime2-conqur-plugin-for-batch-correction-or-alternative/33218 "2025-06-04T04:04:35Z")
Hi all! I recently came across the ConQuR tool (paper, GitHub) for dealing with microbiome batch effects, and it looks pretty useful. I was wondering whether a Qiime2 plugin exists for it, and if not, whether one might… --- ## [Shotgun sequencing and Trimming](https://forum.qiime2.org/t/shotgun-sequencing-and-trimming/33237)
**Author:** [@FRANCESCOMONTESI](https://forum.qiime2.org/u/FRANCESCOMONTESI)\ **Replies:** 2\ **Last updated:** [June 3, 2025, 4:09pm UTC](https://forum.qiime2.org/t/shotgun-sequencing-and-trimming/33237 "2025-06-03T16:09:26Z")
Hi, i'm working with 3 samples of fungi, so i have ITS DNA sequences, reads are 151 bp long and Shotgun DNA sequencing (not amplification with primers) was performed by an external facility. In my code i have demultipl… --- ## [Can I run QIIME2 on de-multiplexed 5R 16S files?](https://forum.qiime2.org/t/can-i-run-qiime2-on-de-multiplexed-5r-16s-files/33241)
**Author:** [@John\_Frame](https://forum.qiime2.org/u/John_Frame)\ **Replies:** 1\ **Last updated:** [June 3, 2025, 1:48pm UTC](https://forum.qiime2.org/t/can-i-run-qiime2-on-de-multiplexed-5r-16s-files/33241 "2025-06-03T13:48:41Z")
Recently received some low-biomass samples sequenced with a 5R 16S protocol. They've already been de-multiplexed. I've run them through the qiime2 dada2 workflow all the way through feature table creation and taxonomic … [Previous page](https://forum.qiime2.org/c/general-discussion/23.md?page=2) [Next page](https://forum.qiime2.org/c/general-discussion/23.md?page=4)