# Ideas and Suggestions **URL:** https://forum.qiime2.org/c/ideas-and-suggestions/9.md?page=4 [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) **Page:** 5 --- ## [Feature-table filter-samples](https://forum.qiime2.org/t/feature-table-filter-samples/5323)
**Author:** [@emescioglu](https://forum.qiime2.org/u/emescioglu)\ **Replies:** 2\ **Last updated:** [August 9, 2018, 7:50pm UTC](https://forum.qiime2.org/t/feature-table-filter-samples/5323 "2018-08-09T19:50:00Z")
Filtering out unwanted samples from a table can result in lots of frequencies that are no longer present in any samples, so your data remains really large with lots of 0's. It would be nice if feature-table filter-sample… --- ## [Additional output for vsearch cluster-features-closed-reference: reads passing OTU picking](https://forum.qiime2.org/t/additional-output-for-vsearch-cluster-features-closed-reference-reads-passing-otu-picking/4276)
**Author:** [@yanxianl](https://forum.qiime2.org/u/yanxianl)\ **Replies:** 3\ **Last updated:** [August 2, 2018, 3:24am UTC](https://forum.qiime2.org/t/additional-output-for-vsearch-cluster-features-closed-reference-reads-passing-otu-picking/4276 "2018-08-02T03:24:49Z")
Hi, As part of quality control, it's often desired to know how well reference-based OTU picking works for our samples by checking the percentage of reads passing the closed-reference OTU picking. Though it's not difficu… --- ## [BLAST parser for assign\_taxonomy](https://forum.qiime2.org/t/blast-parser-for-assign-taxonomy/292)
**Author:** [@SGMcCalla](https://forum.qiime2.org/u/SGMcCalla)\ **Replies:** 13\ **Last updated:** [July 31, 2018, 12:53pm UTC](https://forum.qiime2.org/t/blast-parser-for-assign-taxonomy/292 "2018-07-31T12:53:14Z")
Are there plans to incorporate brocc.py (GitHub - kylebittinger/brocc: Consensus taxonomy assignment for short reads (great for fungi)) into Qiime2 as a plugin? brocc parses BLAST output (in place of assign\_taxonomy) and… --- ## [Emailing a User Upon Completion of Long Tasks such as DADA2 Denoising or Machine Learning Classification](https://forum.qiime2.org/t/emailing-a-user-upon-completion-of-long-tasks-such-as-dada2-denoising-or-machine-learning-classification/5249)
**Author:** [@AlfalfaResearcher](https://forum.qiime2.org/u/AlfalfaResearcher)\ **Replies:** 2\ **Last updated:** [July 25, 2018, 4:18pm UTC](https://forum.qiime2.org/t/emailing-a-user-upon-completion-of-long-tasks-such-as-dada2-denoising-or-machine-learning-classification/5249 "2018-07-25T16:18:48Z")
Hi everyone, In discussions with my labmates we thought it would be really useful if a future version of Qiime could include the ability to automatically email a particular person or group of people. We thought this wou… --- ## [Linking tutorial steps with q2 plugins](https://forum.qiime2.org/t/linking-tutorial-steps-with-q2-plugins/4442)
**Author:** [@Ahmed\_Abdelfattah](https://forum.qiime2.org/u/Ahmed_Abdelfattah)\ **Replies:** 14\ **Last updated:** [July 12, 2018, 8:03pm UTC](https://forum.qiime2.org/t/linking-tutorial-steps-with-q2-plugins/4442 "2018-07-12T20:03:49Z")
Dear qiime2 team, First, congratulations on the excellent work you have done and the tidy organization of the website. I have a suggestion that might be helpful to users, especially beginners. I think it would be nice t… --- ## [Default passwords should be changed](https://forum.qiime2.org/t/default-passwords-should-be-changed/4948)
**Author:** [@mickvav](https://forum.qiime2.org/u/mickvav)\ **Replies:** 1\ **Last updated:** [July 10, 2018, 1:41pm UTC](https://forum.qiime2.org/t/default-passwords-should-be-changed/4948 "2018-07-10T13:41:14Z")
Hello, all. I've recently installed qiime2 on virtual machine and exported it on public IP address, so my student was able to analyse his data on my server. I've performed basic security-related measures myself - change… --- ## [Emperor Plot Visualization on papers and posters](https://forum.qiime2.org/t/emperor-plot-visualization-on-papers-and-posters/4953)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 3\ **Last updated:** [July 10, 2018, 1:20am UTC](https://forum.qiime2.org/t/emperor-plot-visualization-on-papers-and-posters/4953 "2018-07-10T01:20:49Z")
I think it would be really cool if once you create your emperor plot and finish changing all of your settings you could create a QR code. Then you could put this on your posters and/or papers so then people can easily se… --- ## [Canonical Correspondence Analysis](https://forum.qiime2.org/t/canonical-correspondence-analysis/3197)
**Author:** [@emescioglu](https://forum.qiime2.org/u/emescioglu)\ **Replies:** 4\ **Last updated:** [June 27, 2018, 3:55pm UTC](https://forum.qiime2.org/t/canonical-correspondence-analysis/3197 "2018-06-27T15:55:25Z")
Hello, I'm wondering if there are plans to add a canonical correspondence analysis to the diversity plugin. It would be great for the pcoa skeptics :slight\_smile: Thanks! Esra --- ## [Warn if filter-samples returns empty table](https://forum.qiime2.org/t/warn-if-filter-samples-returns-empty-table/4620)
**Author:** [@jjmmii](https://forum.qiime2.org/u/jjmmii)\ **Replies:** 1\ **Last updated:** [June 20, 2018, 12:25am UTC](https://forum.qiime2.org/t/warn-if-filter-samples-returns-empty-table/4620 "2018-06-20T00:25:22Z")
When performing feature-table filter-samples, I often am unaware that the resulting table is empty because of some mistakes in the --p-where clause until I export or summarize the filtered table. It would be great if a w… --- ## [Allowing users to rename exported files from QIIME2 artifact](https://forum.qiime2.org/t/allowing-users-to-rename-exported-files-from-qiime2-artifact/4526)
**Author:** [@yanxianl](https://forum.qiime2.org/u/yanxianl)\ **Replies:** 1\ **Last updated:** [June 13, 2018, 11:44pm UTC](https://forum.qiime2.org/t/allowing-users-to-rename-exported-files-from-qiime2-artifact/4526 "2018-06-13T23:44:52Z")
Hi, When exporting files of the same type, I often have to rename the exported files before I can proceed with the next one as they share the same file name. It'd be great to enable users to rename the exported files in… --- ## [Equivalent to remove PyNAST failures in QIIME2](https://forum.qiime2.org/t/equivalent-to-remove-pynast-failures-in-qiime2/4272)
**Author:** [@calozupone](https://forum.qiime2.org/u/calozupone)\ **Replies:** 12\ **Last updated:** [June 13, 2018, 3:39pm UTC](https://forum.qiime2.org/t/equivalent-to-remove-pynast-failures-in-qiime2/4272 "2018-06-13T15:39:01Z")
Hello, I am working with a dataset that contains some samples with many sequences that would have been removed as PyNAST failures with QIIME1. These sequences (which are unassigned taxonomically when running through gre… --- ## [Using non-integer data with beta diversity](https://forum.qiime2.org/t/using-non-integer-data-with-beta-diversity/4453)
**Author:** [@wasade](https://forum.qiime2.org/u/wasade)\ **Replies:** 3\ **Last updated:** [June 7, 2018, 5:07pm UTC](https://forum.qiime2.org/t/using-non-integer-data-with-beta-diversity/4453 "2018-06-07T17:07:24Z")
I'm working with @vrbana on some metabolomics data. These data are expressed as floating point values and do not make sense to express as integers. When using qiime diversity beta, we were getting tracebacks indicating t… --- ## [Annotation/Comments option for artifacts](https://forum.qiime2.org/t/annotation-comments-option-for-artifacts/3949)
**Author:** [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)\ **Replies:** 4\ **Last updated:** [April 27, 2018, 4:48pm UTC](https://forum.qiime2.org/t/annotation-comments-option-for-artifacts/3949 "2018-04-27T16:48:37Z")
First off, big congrats on the release of qiime 2018.4 :fireworks::tropical\_drink:! With the ever growing number of options and branches of the available pipelines I was thinking it might now be useful to have an annotat… --- ## [Metadata quickstart tutorial](https://forum.qiime2.org/t/metadata-quickstart-tutorial/3910)
**Author:** [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\ **Replies:** 1\ **Last updated:** [April 25, 2018, 9:30pm UTC](https://forum.qiime2.org/t/metadata-quickstart-tutorial/3910 "2018-04-25T21:30:25Z")
The metadata tutorial is very detailed and comprehensive. It's also a little imposing for first time users. I would love to see some sort of 'Metadata cheat sheet' that leads with a good example. Qiime 1 did a pretty go… --- ## [White space parsing issue in manifest](https://forum.qiime2.org/t/white-space-parsing-issue-in-manifest/3847)
**Author:** [@tengfey](https://forum.qiime2.org/u/tengfey)\ **Replies:** 2\ **Last updated:** [April 19, 2018, 12:47am UTC](https://forum.qiime2.org/t/white-space-parsing-issue-in-manifest/3847 "2018-04-19T00:47:10Z")
I noticed that if there is whitespace at the end of a manifest file, it will raise errors like this qiime tools import --type 'SampleData\[PairedEndSequencesWithQuality\]' --input-path cancer10-manifest --output-pat… --- ## [Feature-table heatmap with no clustering on neither axes](https://forum.qiime2.org/t/feature-table-heatmap-with-no-clustering-on-neither-axes/3826)
**Author:** [@jjmmii](https://forum.qiime2.org/u/jjmmii)\ **Replies:** 1\ **Last updated:** [April 18, 2018, 9:44pm UTC](https://forum.qiime2.org/t/feature-table-heatmap-with-no-clustering-on-neither-axes/3826 "2018-04-18T21:44:45Z")
Occasionally it is useful to compare different heatmaps without clustering on neither samples nor feature axes, so that their order stays the same. So far feature-table heatmap must specify at least one axis to cluster. … --- ## [Qiime2 (2018.2.0) vs Qiime 1 (1.9)](https://forum.qiime2.org/t/qiime2-2018-2-0-vs-qiime-1-1-9/3541)
**Author:** [@Nishat\_Tasnim](https://forum.qiime2.org/u/Nishat_Tasnim)\ **Replies:** 4\ **Last updated:** [April 16, 2018, 11:13pm UTC](https://forum.qiime2.org/t/qiime2-2018-2-0-vs-qiime-1-1-9/3541 "2018-04-16T23:13:30Z")
Wondering if there are existing documents comparing Qiime1 versus Qiime2 pipelines, including information comparisons of plugins/versions, and input&generated file formats? If not, I'll be creating my own documents over … --- ## [Adding more configurations to taxa-bar-plots.qzv](https://forum.qiime2.org/t/adding-more-configurations-to-taxa-bar-plots-qzv/1920)
**Author:** [@yanxianl](https://forum.qiime2.org/u/yanxianl)\ **Replies:** 2\ **Last updated:** [November 21, 2017, 1:59pm UTC](https://forum.qiime2.org/t/adding-more-configurations-to-taxa-bar-plots-qzv/1920 "2017-11-21T13:59:07Z")
Hello, After exploring the taxa bar plots for a while, I have one suggetion that I think will improve user experience. Can users choose to show only part of the taxa so that we don't need to download the csv file and m… --- ## [Q2-cutadapt Log](https://forum.qiime2.org/t/q2-cutadapt-log/2584)
**Author:** [@michoug](https://forum.qiime2.org/u/michoug)\ **Replies:** 5\ **Last updated:** [April 9, 2018, 6:37pm UTC](https://forum.qiime2.org/t/q2-cutadapt-log/2584 "2018-04-09T18:37:11Z")
Hi Is it possible to add an option to print/save the log of the software? I just want to be sure that all the reads contained the primers that I want to remove. This information was shown in the "original" cutadapt so… --- ## [Adding metadata tags to feature-table visualizations](https://forum.qiime2.org/t/adding-metadata-tags-to-feature-table-visualizations/3583)
**Author:** [@wsano](https://forum.qiime2.org/u/wsano)\ **Replies:** 2\ **Last updated:** [April 6, 2018, 3:39am UTC](https://forum.qiime2.org/t/adding-metadata-tags-to-feature-table-visualizations/3583 "2018-04-06T03:39:07Z")
My sample IDs, for the sake of uniformity within a specific project, usually look something like WS001, WS002, WS003, etc...., so a sample ID by itself isn't that informative. When looking at feature-table.qzv files in Q… --- ## [Feature-classifier classify-consensus-blast should have a cutoff for query cover](https://forum.qiime2.org/t/feature-classifier-classify-consensus-blast-should-have-a-cutoff-for-query-cover/3641)
**Author:** [@dwt](https://forum.qiime2.org/u/dwt)\ **Replies:** 1\ **Last updated:** [April 3, 2018, 3:15pm UTC](https://forum.qiime2.org/t/feature-classifier-classify-consensus-blast-should-have-a-cutoff-for-query-cover/3641 "2018-04-03T15:15:29Z")
Which causes blast to select short (~20 bp) alignments with high percent ID rather than Unassigned For example here is a taxonomy.qzv and rep\_seqs.qzv: https://drive.google.com/open?id=11jvC1flUSAgLOe7rSTIP\_qw9MgKOHYOE … --- ## [Taxa barplot lock name after hover and click](https://forum.qiime2.org/t/taxa-barplot-lock-name-after-hover-and-click/3550)
**Author:** [@jjmmii](https://forum.qiime2.org/u/jjmmii)\ **Replies:** 1\ **Last updated:** [March 26, 2018, 10:57pm UTC](https://forum.qiime2.org/t/taxa-barplot-lock-name-after-hover-and-click/3550 "2018-03-26T22:57:44Z")
Hello, when I spot a taxa of interest on a taxa barplot, I would hover my mouse on the bar to see its name. But when I move my mouse to copy it, the name changes to something else because my mouse passes through other ba… --- ## [Import Casava demultiplexed sequences with project name](https://forum.qiime2.org/t/import-casava-demultiplexed-sequences-with-project-name/3440)
**Author:** [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)\ **Replies:** 1\ **Last updated:** [March 16, 2018, 8:17pm UTC](https://forum.qiime2.org/t/import-casava-demultiplexed-sequences-with-project-name/3440 "2018-03-16T20:17:26Z")
Im working with paired end reads that were demultiplexed using Casava. The file name follows the format of \[project id\]\\\_\[sample id with underscore\]\_L001\_\[read id\]\_001.fastq For instance, p01\_s01\_20180315\_L001\_R1\_001.fa… --- ## [Better location information for "utf-8 can't decode codec..." error](https://forum.qiime2.org/t/better-location-information-for-utf-8-cant-decode-codec-error/2113)
**Author:** [@nick-youngblut](https://forum.qiime2.org/u/nick-youngblut)\ **Replies:** 7\ **Last updated:** [February 16, 2018, 4:57pm UTC](https://forum.qiime2.org/t/better-location-information-for-utf-8-cant-decode-codec-error/2113 "2018-02-16T16:57:22Z")
My metadata table seems to contain \>=1 non-ASCII character, so when I try to use it for commands such as qiime taxa barplot, I get the following error: There was an issue with loading the file /path/to/my/file/metadata.… --- ## [Beta-group-significance plots not representative of PERMANOVA test](https://forum.qiime2.org/t/beta-group-significance-plots-not-representative-of-permanova-test/3320)
**Author:** [@CarlyRae](https://forum.qiime2.org/u/CarlyRae)\ **Replies:** 2\ **Last updated:** [March 8, 2018, 8:23pm UTC](https://forum.qiime2.org/t/beta-group-significance-plots-not-representative-of-permanova-test/3320 "2018-03-08T20:23:09Z")
Hi, I attended the QIIME 2.0 workshop at NIH. It was a great opportunity to learn a lot about the new features of QIIME 2.0. I had one suggestion. For the qiime diversity beta-group-significance command, in the visualiz… --- ## [Possible to set '--fasta\_width 0' for consistency with other plugins?](https://forum.qiime2.org/t/possible-to-set-fasta-width-0-for-consistency-with-other-plugins/3204)
**Author:** [@Chris\_Hemmerich](https://forum.qiime2.org/u/Chris_Hemmerich)\ **Replies:** 1\ **Last updated:** [February 27, 2018, 8:46pm UTC](https://forum.qiime2.org/t/possible-to-set-fasta-width-0-for-consistency-with-other-plugins/3204 "2018-02-27T20:46:35Z")
I used the uchime-denovo command from the vsearch plugin in a recent workflow and it identified additional chimeras beyond DADA2. Nice. However, I ran into a hiccup when exporting nonchimeras.qza to a fasta file in that … --- ## [Support FeatureTable\[PresenceAbsence\] for qualitative metrics/indices?](https://forum.qiime2.org/t/support-featuretable-presenceabsence-for-qualitative-metrics-indices/3225)
**Author:** [@ebolyen](https://forum.qiime2.org/u/ebolyen)\ **Replies:** 0\ **Last updated:** [February 27, 2018, 8:03pm UTC](https://forum.qiime2.org/t/support-featuretable-presenceabsence-for-qualitative-metrics-indices/3225 "2018-02-27T20:03:37Z")
I'm working with the precomputed PICRUSt KEGG/GG tables and I am interested in doing some hierarchical clustering of the GG features based on their functional profiles. To do that, I would need some kind of distance, bu… --- ## [Possible to provide warning when metadata doesn't have a header?](https://forum.qiime2.org/t/possible-to-provide-warning-when-metadata-doesnt-have-a-header/1450)
**Author:** [@Chris\_Hemmerich](https://forum.qiime2.org/u/Chris_Hemmerich)\ **Replies:** 8\ **Last updated:** [February 26, 2018, 7:53pm UTC](https://forum.qiime2.org/t/possible-to-provide-warning-when-metadata-doesnt-have-a-header/1450 "2018-02-26T19:53:58Z")
In my rush to try out the new filter-seqs command I made a bit of a headache for myself by not having a header line in my metadata and losing my first sequence. I wasn't using a where clause, so just using the first colu… --- ## [Adding download option for FDR-adjusted p.value table in gneiss](https://forum.qiime2.org/t/adding-download-option-for-fdr-adjusted-p-value-table-in-gneiss/2995)
**Author:** [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)\ **Replies:** 1\ **Last updated:** [February 25, 2018, 8:00pm UTC](https://forum.qiime2.org/t/adding-download-option-for-fdr-adjusted-p-value-table-in-gneiss/2995 "2018-02-25T20:00:41Z")
Just wanted to raise a separate issue on this in hope of having this function added. Continuing the discussion from Gneiss questions: I'm working with a dataset that has a large number of balances to the point where t… --- ## [q2-cutadapt add option --discard-untrimmed](https://forum.qiime2.org/t/q2-cutadapt-add-option-discard-untrimmed/3124)
**Author:** [@michoug](https://forum.qiime2.org/u/michoug)\ **Replies:** 0\ **Last updated:** [February 21, 2018, 6:12pm UTC](https://forum.qiime2.org/t/q2-cutadapt-add-option-discard-untrimmed/3124 "2018-02-21T18:12:06Z")
Hi Is it possible to add the "--discard-untrimmed" command of the standalone cutadapt software to q2-cutadapt in order to remove reads that don't have the adapters? Best Greg [Previous page](https://forum.qiime2.org/c/ideas-and-suggestions/9.md?page=3) [Next page](https://forum.qiime2.org/c/ideas-and-suggestions/9.md?page=5)