# Ideas and Suggestions **URL:** https://forum.qiime2.org/c/ideas-and-suggestions/9.md?page=2 [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) **Page:** 3 --- ## [Get an r^2 value when running a PERMANOVA test](https://forum.qiime2.org/t/get-an-r-2-value-when-running-a-permanova-test/7392)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 3\ **Last updated:** [August 14, 2020, 6:58pm UTC](https://forum.qiime2.org/t/get-an-r-2-value-when-running-a-permanova-test/7392 "2020-08-14T18:58:34Z")
When running a PERMANOVA test, other programs will also give you an r^2 value (such as Primer). It would be nice if Qiime2 would give you an r^2 value (for example) when calculating the p-values for beta group significan… --- ## [Joint filtering for a feature table](https://forum.qiime2.org/t/joint-filtering-for-a-feature-table/14230)
**Author:** [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)\ **Replies:** 2\ **Last updated:** [August 5, 2020, 4:43pm UTC](https://forum.qiime2.org/t/joint-filtering-for-a-feature-table/14230 "2020-08-05T16:43:29Z")
Hi lovely people, I know this has been thrown around somewhere, but I'd love to add the ability to do a filter based on some combination of prevalence and abundance (i.e. given that a feature has X relative abundance in… --- ## [QIIME 2 Artifact Caching](https://forum.qiime2.org/t/qiime-2-artifact-caching/8792)
**Author:** [@ebolyen](https://forum.qiime2.org/u/ebolyen)\ **Replies:** 7\ **Last updated:** [July 13, 2020, 5:46pm UTC](https://forum.qiime2.org/t/qiime-2-artifact-caching/8792 "2020-07-13T17:46:43Z")
I was talking to @thermokarst the other day about how we might be able to cache things like database index files, and I wanted to write it down here (for input and so we don't forget). What if there was a user managed a… --- ## [Filtering method for FeatureData\[Differential\]](https://forum.qiime2.org/t/filtering-method-for-featuredata-differential/15553)
**Author:** [@dwt](https://forum.qiime2.org/u/dwt)\ **Replies:** 2\ **Last updated:** [July 6, 2020, 12:54pm UTC](https://forum.qiime2.org/t/filtering-method-for-featuredata-differential/15553 "2020-07-06T12:54:11Z")
Hi all, As far as I can see there are not methods for filtering FeatureData\[Differential\] artifacts, like those created by songbird. I've run into needing this because when running qurro if you filter the table to only… --- ## [Open multiple .qzv files on Qiime2 view at once](https://forum.qiime2.org/t/open-multiple-qzv-files-on-qiime2-view-at-once/15100)
**Author:** [@michael-nakai](https://forum.qiime2.org/u/michael-nakai)\ **Replies:** 5\ **Last updated:** [June 9, 2020, 3:27am UTC](https://forum.qiime2.org/t/open-multiple-qzv-files-on-qiime2-view-at-once/15100 "2020-06-09T03:27:52Z")
I'm currently working on a dataset with many metadata variables, so I end up with many qzv files after running beta-analyses and other analyses on the dataset. When viewing them on Qiime2 view, I have to drag them in one… --- ## [Tool for storing and debugging QIIME2 codes](https://forum.qiime2.org/t/tool-for-storing-and-debugging-qiime2-codes/14449)
**Author:** [@Negin](https://forum.qiime2.org/u/Negin)\ **Replies:** 3\ **Last updated:** [May 10, 2020, 3:42am UTC](https://forum.qiime2.org/t/tool-for-storing-and-debugging-qiime2-codes/14449 "2020-05-10T03:42:11Z")
Hi all, I am wondering if there is a tool similar to Atom or Virtual Code Studio that is specific to QIIME2 codes. I know QIIME2 has been written in Python but it does not necessary follow Python rules so we cannot set … --- ## [mafft --large argument support](https://forum.qiime2.org/t/mafft-large-argument-support/14564)
**Author:** [@Deni\_Ribicic](https://forum.qiime2.org/u/Deni_Ribicic)\ **Replies:** 2\ **Last updated:** [April 20, 2020, 9:46pm UTC](https://forum.qiime2.org/t/mafft-large-argument-support/14564 "2020-04-20T21:46:32Z")
Dear developers, I think it would be handy to have mafft --large option available. Many people, including myself are taking advantage of q2 pipeline to process long 16S rRNA reads generated by Oxford Nanopore technolog… --- ## [right-trim option in extract-reads for paired-end data?](https://forum.qiime2.org/t/right-trim-option-in-extract-reads-for-paired-end-data/14191)
**Author:** [@Sean\_McKenzie](https://forum.qiime2.org/u/Sean_McKenzie)\ **Replies:** 2\ **Last updated:** [March 24, 2020, 9:06pm UTC](https://forum.qiime2.org/t/right-trim-option-in-extract-reads-for-paired-end-data/14191 "2020-03-24T21:06:43Z")
Hello, no idea if this is the appropriate way to make a feature request, but it seems problematic that (as far as I can tell) there's no way to trim some base-pairs from the right side of the extracted reads (using extra… --- ## [create NCBI database](https://forum.qiime2.org/t/create-ncbi-database/12671)
**Author:** [@thedam](https://forum.qiime2.org/u/thedam)\ **Replies:** 6\ **Last updated:** [December 17, 2019, 8:23pm UTC](https://forum.qiime2.org/t/create-ncbi-database/12671 "2019-12-17T20:23:59Z")
Hey, I'd like to use NCBI database for classification. I can find taxonomy/sequences for Silva and GreenGenes, but there's no any hints how to create such NCBI-based database. Any suggestion how to perform it? Should I… --- ## [Faiths Phylogenetic Diversity Boxplot](https://forum.qiime2.org/t/faiths-phylogenetic-diversity-boxplot/12837)
**Author:** [@Arun04](https://forum.qiime2.org/u/Arun04)\ **Replies:** 2\ **Last updated:** [December 12, 2019, 6:26am UTC](https://forum.qiime2.org/t/faiths-phylogenetic-diversity-boxplot/12837 "2019-12-12T06:26:29Z")
Dear all, I have generated my Faiths PD boxplot. I realised that the x-axis is not sorted properly. Is there any way to get the axes sorted in correct order? Thank you. --- ## [Merging Metadata for Meta-Analysis](https://forum.qiime2.org/t/merging-metadata-for-meta-analysis/5752)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 2\ **Last updated:** [August 27, 2018, 2:55pm UTC](https://forum.qiime2.org/t/merging-metadata-for-meta-analysis/5752 "2018-08-27T14:55:17Z")
It would be nice if there was a command that would be able to merge 2 metadata files from different studies. It could check for the columns that aren't present in both and fill the samples that didn't collect this inform… --- ## [Taxonomic assignations](https://forum.qiime2.org/t/taxonomic-assignations/12561)
**Author:** [@mamunnoz](https://forum.qiime2.org/u/mamunnoz)\ **Replies:** 3\ **Last updated:** [November 21, 2019, 9:46am UTC](https://forum.qiime2.org/t/taxonomic-assignations/12561 "2019-11-21T09:46:42Z")
Doing taxonomic assignations with sklearn and a fit classifier is easy to obtain incongruencies. For example, two sequences very similar, being probably the same taxon can be classify as different taxons if one is very s… --- ## [Color correction in gneiss balance-taxonomy](https://forum.qiime2.org/t/color-correction-in-gneiss-balance-taxonomy/7218)
**Author:** [@Ravenclaw](https://forum.qiime2.org/u/Ravenclaw)\ **Replies:** 3\ **Last updated:** [October 25, 2019, 2:21am UTC](https://forum.qiime2.org/t/color-correction-in-gneiss-balance-taxonomy/7218 "2019-10-25T02:21:50Z")
Hi In the output for gneiss balance-taxonomy, the colors used for the different categories are switched in the log ratio plot and the proportion plot. Here is an example. Its a minor thing but could be confusing. Im usi… --- ## [q2view on mobile devices](https://forum.qiime2.org/t/q2view-on-mobile-devices/10821)
**Author:** [@BenKaehler](https://forum.qiime2.org/u/BenKaehler)\ **Replies:** 4\ **Last updated:** [October 10, 2019, 9:47pm UTC](https://forum.qiime2.org/t/q2view-on-mobile-devices/10821 "2019-10-10T21:47:23Z")
Hello QIIME 2 Forum, Long time listener first time caller. I would like to use a mobile device (an iPad) to present q2view to an audience. q2view does not work well on my device. It refuses to load in most browsers (t… --- ## [Suggested answers to tutorial questions?](https://forum.qiime2.org/t/suggested-answers-to-tutorial-questions/11774)
**Author:** [@Bethanie](https://forum.qiime2.org/u/Bethanie)\ **Replies:** 1\ **Last updated:** [October 1, 2019, 4:43pm UTC](https://forum.qiime2.org/t/suggested-answers-to-tutorial-questions/11774 "2019-10-01T16:43:28Z")
Hi, I am new to Qiime and microbiome research in general, I am enjoying working through the tutorials but it is impossible to know the whether my answers to the questions are correct (and there's not really anyone I can… --- ## [Q2-longitudinal LME graphics](https://forum.qiime2.org/t/q2-longitudinal-lme-graphics/11531)
**Author:** [@linama](https://forum.qiime2.org/u/linama)\ **Replies:** 2\ **Last updated:** [September 16, 2019, 7:47pm UTC](https://forum.qiime2.org/t/q2-longitudinal-lme-graphics/11531 "2019-09-16T19:47:59Z")
Hi All, I am doing some longitudinal analysis using q2- longitudinal. I would like to have all Regression scatterplots at the same scale (y-axis). Is it possible to do that? I'm using version QIIME2, release 2018.11. T… --- ## [Consider adding the check of the reversed keywords for SQL in keemei](https://forum.qiime2.org/t/consider-adding-the-check-of-the-reversed-keywords-for-sql-in-keemei/10855)
**Author:** [@wenching](https://forum.qiime2.org/u/wenching)\ **Replies:** 0\ **Last updated:** [July 26, 2019, 5:35pm UTC](https://forum.qiime2.org/t/consider-adding-the-check-of-the-reversed-keywords-for-sql-in-keemei/10855 "2019-07-26T17:35:35Z")
When ran qiime feature-table filter-samples to remove samples without values, the following warning raised due to the use of reserved keywords as feature names in my metadata table. If one of the metadata column names s… --- ## [Add DADA2 parameters](https://forum.qiime2.org/t/add-dada2-parameters/8345)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 3\ **Last updated:** [July 17, 2019, 12:37pm UTC](https://forum.qiime2.org/t/add-dada2-parameters/8345 "2019-07-17T12:37:01Z")
My labmate and I have been working with a set of data where we are specifically interested in more rare OTUs. However, when running DADA2 via QIIME2, we noticed that if an OTU is only found once in a sample (or even foun… --- ## [Filtering a feature-table and its rep-seqs file simultaneously.](https://forum.qiime2.org/t/filtering-a-feature-table-and-its-rep-seqs-file-simultaneously/10562)
**Author:** [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)\ **Replies:** 0\ **Last updated:** [July 6, 2019, 9:16pm UTC](https://forum.qiime2.org/t/filtering-a-feature-table-and-its-rep-seqs-file-simultaneously/10562 "2019-07-06T21:16:27Z")
This is just a minor convenience suggestion. When one filters features from a feature-table it is often desirable -recommended even- to remove those same features from the corresponding rep-seqs file in a second step. W… --- ## [Executable pipeline from artifact/visualization provenance](https://forum.qiime2.org/t/executable-pipeline-from-artifact-visualization-provenance/10436)
**Author:** [@Hunter\_Cameron](https://forum.qiime2.org/u/Hunter_Cameron)\ **Replies:** 1\ **Last updated:** [July 1, 2019, 4:22pm UTC](https://forum.qiime2.org/t/executable-pipeline-from-artifact-visualization-provenance/10436 "2019-07-01T16:22:06Z")
I was wondering if it would be of interest to have the ability to extract the qiime2 commands needed to rerun a workflow from an artifact's proveneance? Does this already exist? The envisioned use case is for reproducin… --- ## [Suggestion: Allow users to access their posts during moderation.](https://forum.qiime2.org/t/suggestion-allow-users-to-access-their-posts-during-moderation/10399)
**Author:** [@abalter](https://forum.qiime2.org/u/abalter)\ **Replies:** 1\ **Last updated:** [June 24, 2019, 9:26pm UTC](https://forum.qiime2.org/t/suggestion-allow-users-to-access-their-posts-during-moderation/10399 "2019-06-24T21:26:33Z")
Quick suggestion: I just signed up and made my first post. I wanted to go over it and make sure all the markup looks good and generally give it another once over. However, I wasn't able to preview it, and it does not s… --- ## [Multiple V-regions amplicons](https://forum.qiime2.org/t/multiple-v-regions-amplicons/10109)
**Author:** [@chaibenl](https://forum.qiime2.org/u/chaibenl)\ **Replies:** 3\ **Last updated:** [June 7, 2019, 4:38pm UTC](https://forum.qiime2.org/t/multiple-v-regions-amplicons/10109 "2019-06-07T16:38:40Z")
Can we use Qiime2 to estimate microbial community composition from amplicon reads of multiple 16S V-regions? --- ## [QIIME 2 Workshop in Brazil?](https://forum.qiime2.org/t/qiime-2-workshop-in-brazil/9906)
**Author:** [@Ondina\_Palmeira](https://forum.qiime2.org/u/Ondina_Palmeira)\ **Replies:** 2\ **Last updated:** [June 3, 2019, 5:23pm UTC](https://forum.qiime2.org/t/qiime-2-workshop-in-brazil/9906 "2019-06-03T17:23:44Z")
Hello! Any chance of a workshop taking place in Brazil, Sao Paulo? Regards! --- ## [Why pyNAST is no longer available in QIIME2?](https://forum.qiime2.org/t/why-pynast-is-no-longer-available-in-qiime2/9464)
**Author:** [@ynshen](https://forum.qiime2.org/u/ynshen)\ **Replies:** 3\ **Last updated:** [May 31, 2019, 10:25pm UTC](https://forum.qiime2.org/t/why-pynast-is-no-longer-available-in-qiime2/9464 "2019-05-31T22:25:04Z")
Hi, I am QIIME 1 user and have been using pyNAST as one of the filters to remove reads not from 16s rRNA in the samples – I found it performed pretty well for my datasets. I wonder why pyNAST is no longer available in Q… --- ## [Dada2 minimum overlap](https://forum.qiime2.org/t/dada2-minimum-overlap/9917)
**Author:** [@timanix](https://forum.qiime2.org/u/timanix)\ **Replies:** 4\ **Last updated:** [May 26, 2019, 3:45pm UTC](https://forum.qiime2.org/t/dada2-minimum-overlap/9917 "2019-05-26T15:45:57Z")
Hi! I was wondering, is there any way to set minimum overlap for merging the reads in q2-DADA2 for paired reads? Like minOverlap in R. Just to be able to compare the outputs with default 12 bases and custom parameter. --- ## [Updating DADA2 to Latest Version](https://forum.qiime2.org/t/updating-dada2-to-latest-version/8556)
**Author:** [@AlfalfaResearcher](https://forum.qiime2.org/u/AlfalfaResearcher)\ **Replies:** 2\ **Last updated:** [March 5, 2019, 3:49pm UTC](https://forum.qiime2.org/t/updating-dada2-to-latest-version/8556 "2019-03-05T15:49:24Z")
Curious to know if there are plans to update the DADA2 package used in QIIME2. Just saw that DADA2 is up to version 1.10. QIIME2 currently uses version 1.6.0. --- ## [Detecting FASTQ variant types](https://forum.qiime2.org/t/detecting-fastq-variant-types/1252)
**Author:** [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)\ **Replies:** 5\ **Last updated:** [May 13, 2019, 11:15pm UTC](https://forum.qiime2.org/t/detecting-fastq-variant-types/1252 "2019-05-13T23:15:35Z")
As briefly suggested here just starting a discussion as whether its possible to implement some sort of fastq variant detection method for those cases where an unknown fastq file is inherited to the user. The closest to… --- ## [Procrustes analysis: p-value](https://forum.qiime2.org/t/procrustes-analysis-p-value/9184)
**Author:** [@bsen2018](https://forum.qiime2.org/u/bsen2018)\ **Replies:** 4\ **Last updated:** [April 10, 2019, 1:48pm UTC](https://forum.qiime2.org/t/procrustes-analysis-p-value/9184 "2019-04-10T13:48:27Z")
Hello! I was recently testing the Procrustes analysis in Qiime2 using these two methods: procrustes\_analysis and procrustes\_plot. The plot was generated successfully. Yet, it would be nice if we can also obtain the p-va… --- ## [Multi-level taxa barplots](https://forum.qiime2.org/t/multi-level-taxa-barplots/9145)
**Author:** [@wsano](https://forum.qiime2.org/u/wsano)\ **Replies:** 1\ **Last updated:** [April 8, 2019, 6:32pm UTC](https://forum.qiime2.org/t/multi-level-taxa-barplots/9145 "2019-04-08T18:32:08Z")
I like how barplot.qzv files let me click on taxa in my legend and see where those bacteria pop up in my barplot, but it becomes difficult to track, say, Rhizobiales in a barplot of order relative abundance once I switch… --- ## [Proposal for new QIIME 2 community code of conduct](https://forum.qiime2.org/t/proposal-for-new-qiime-2-community-code-of-conduct/8213)
**Author:** [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)\ **Replies:** 2\ **Last updated:** [March 28, 2019, 6:00pm UTC](https://forum.qiime2.org/t/proposal-for-new-qiime-2-community-code-of-conduct/8213 "2019-03-28T18:00:36Z")
Hello QIIME 2 community members, I'd like to propose a new code of conduct for the QIIME 2 community. In the last two QIIME 2 workshops that I've taught, all of the instructors agreed to abide by this code of conduct. I… [Previous page](https://forum.qiime2.org/c/ideas-and-suggestions/9.md?page=1) [Next page](https://forum.qiime2.org/c/ideas-and-suggestions/9.md?page=3)