# \#quality **URL:** https://forum.qiime2.org/tag/quality/115.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [QIIME 2 processing of MiSeq i100 data with constant quality scores](https://forum.qiime2.org/t/qiime-2-processing-of-miseq-i100-data-with-constant-quality-scores/34199)
**Author:** [@Kat](https://forum.qiime2.org/u/Kat)\ **Replies:** 3\ **Last updated:** [June 8, 2026, 6:06pm UTC](https://forum.qiime2.org/t/qiime-2-processing-of-miseq-i100-data-with-constant-quality-scores/34199 "2026-06-08T18:06:57Z")
Hi all, Apologies for raising a question that has already been discussed in previous threads, but I am still unsure how to proceed with my dataset. Related posts: New Illumina i100 system data output question. QIIME2… --- ## [wird quality check plots](https://forum.qiime2.org/t/wird-quality-check-plots/32722)
**Author:** [@Sue](https://forum.qiime2.org/u/Sue)\ **Replies:** 6\ **Last updated:** [March 18, 2025, 2:11pm UTC](https://forum.qiime2.org/t/wird-quality-check-plots/32722 "2025-03-18T14:11:57Z")
Hello, We recently changed our data provider, and I’m noticing some unusually high-quality scores in certain blocks. Could this indicate a problem with my data? I’m currently running the following commands: qiime tools… --- ## [Quality interactive plot - demux sequences](https://forum.qiime2.org/t/quality-interactive-plot-demux-sequences/30360)
**Author:** [@abdulghafar](https://forum.qiime2.org/u/abdulghafar)\ **Replies:** 2\ **Last updated:** [June 3, 2024, 4:29pm UTC](https://forum.qiime2.org/t/quality-interactive-plot-demux-sequences/30360 "2024-06-03T16:29:15Z")
I have recently received my paired-end sequence data for targeted amplicon sequencing of 18S region of eukaryotes and the quality plots seem unusual (at least to me since I have seen most of the plots used to be differen… --- ## [Quality Plot Confusion](https://forum.qiime2.org/t/quality-plot-confusion/29490)
**Author:** [@Nadine\_Veasley](https://forum.qiime2.org/u/Nadine_Veasley)\ **Replies:** 3\ **Last updated:** [March 7, 2024, 8:56am UTC](https://forum.qiime2.org/t/quality-plot-confusion/29490 "2024-03-07T08:56:29Z")
Hi! I had went to view my demux.qzv file and this is the quality plot that I was given. I haven't seen one that looks like this before. I was wondering if it looked ok and where it would be plausible to truncate since th… --- ## [Bad reverse plot quality](https://forum.qiime2.org/t/bad-reverse-plot-quality/28409)
**Author:** [@jara\_montibeller](https://forum.qiime2.org/u/jara_montibeller)\ **Replies:** 1\ **Last updated:** [November 24, 2023, 11:38pm UTC](https://forum.qiime2.org/t/bad-reverse-plot-quality/28409 "2023-11-24T23:38:00Z")
Hello everyone, I've imported all of my data and have reached the quality scores plot. It appears that my reverse sequences are showing poor quality, but I'm unsure why this has occurred. Does anyone have any insights … --- ## [Confusing quality plot](https://forum.qiime2.org/t/confusing-quality-plot/27301)
**Author:** [@Zubidiego](https://forum.qiime2.org/u/Zubidiego)\ **Replies:** 3\ **Last updated:** [August 3, 2023, 11:15pm UTC](https://forum.qiime2.org/t/confusing-quality-plot/27301 "2023-08-03T23:15:12Z")
Hello everyone! I am starting to work with a set of 155 samples of V4 region of 16s rRNA that was sequenced using Illumina. I impoted all my data and reached the quality scores plot using QIIME2 2023.5 in conda, but it … --- ## [Bad quality - plot quality](https://forum.qiime2.org/t/bad-quality-plot-quality/24448)
**Author:** [@jara\_montibeller](https://forum.qiime2.org/u/jara_montibeller)\ **Replies:** 4\ **Last updated:** [October 22, 2022, 2:07pm UTC](https://forum.qiime2.org/t/bad-quality-plot-quality/24448 "2022-10-22T14:07:11Z")
I everyone! I imported my all data and I reached the quality scores plot. Here, it seems to me that my sequences are terrible... However, I am not sure about how problematic this can be... What can cause this poor qua… --- ## [NovaSeq6000 with new RTA3 quality scores and DADA2](https://forum.qiime2.org/t/novaseq6000-with-new-rta3-quality-scores-and-dada2/20305)
**Author:** [@mfbeuq](https://forum.qiime2.org/u/mfbeuq)\ **Replies:** 1\ **Last updated:** [July 27, 2021, 7:44am UTC](https://forum.qiime2.org/t/novaseq6000-with-new-rta3-quality-scores-and-dada2/20305 "2021-07-27T07:44:05Z")
Hi guys, I've encountered problems when using reads from NovaSeq 6000 with dada2. The thing is that this system uses a different kind of quality score system: To generate the Q-table for the NovaSeq System, three group… --- ## [The value of mean length after dada2 is too different from the expected value](https://forum.qiime2.org/t/the-value-of-mean-length-after-dada2-is-too-different-from-the-expected-value/19007)
**Author:** [@LiyingXie](https://forum.qiime2.org/u/LiyingXie)\ **Replies:** 10\ **Last updated:** [April 13, 2021, 2:37pm UTC](https://forum.qiime2.org/t/the-value-of-mean-length-after-dada2-is-too-different-from-the-expected-value/19007 "2021-04-13T14:37:41Z")
Hello everyone， I'm a beginner of qiime2, and I'm practicing processing a batch of bacteria data. But after dada2, there are some problems. First of all, I import the data optimized and spliced by sequencing company as … --- ## [MiSeq output quality distribution.](https://forum.qiime2.org/t/miseq-output-quality-distribution/16689)
**Author:** [@rsak-384](https://forum.qiime2.org/u/rsak-384)\ **Replies:** 0\ **Last updated:** [September 24, 2020, 2:23pm UTC](https://forum.qiime2.org/t/miseq-output-quality-distribution/16689 "2020-09-24T14:23:05Z")
Hello. Even though these graphs are produced by qiime2 (2020.8), the question is about the sequences themselves or the sequencing process, not the plugin output. When performing 16S V3-V4 analysis on two different samp… --- ## [Quality in reads suddenly decreases with no apparent reason](https://forum.qiime2.org/t/quality-in-reads-suddenly-decreases-with-no-apparent-reason/15758)
**Author:** [@mfbeuq](https://forum.qiime2.org/u/mfbeuq)\ **Replies:** 5\ **Last updated:** [August 20, 2020, 8:03pm UTC](https://forum.qiime2.org/t/quality-in-reads-suddenly-decreases-with-no-apparent-reason/15758 "2020-08-20T20:03:13Z")
Hey guys, I recently started a new project with 2x250bp Illumina Reads. My FastQC files for the forward reads looked all pretty decent: I then separate my reads into my specific libraries using cutadapt and furtherm… --- ## [Demux summary qzv's Q scores doesn't match the csv when downloaded](https://forum.qiime2.org/t/demux-summary-qzvs-q-scores-doesnt-match-the-csv-when-downloaded/12315)
**Author:** [@KingReyRoi](https://forum.qiime2.org/u/KingReyRoi)\ **Replies:** 3\ **Last updated:** [November 12, 2019, 11:35pm UTC](https://forum.qiime2.org/t/demux-summary-qzvs-q-scores-doesnt-match-the-csv-when-downloaded/12315 "2019-11-12T23:35:29Z")
I imported and demultiplexed my sequences, and now i'm using the summary in order to check out the q-scores in order to filter via dada2. I wanted something more precise than just hovering my mouse over the barplot it gi… --- ## [demux.qzv interpretation for dada2 and/or deblur](https://forum.qiime2.org/t/demux-qzv-interpretation-for-dada2-and-or-deblur/11896)
**Author:** [@ET1335](https://forum.qiime2.org/u/ET1335)\ **Replies:** 6\ **Last updated:** [October 17, 2019, 2:09am UTC](https://forum.qiime2.org/t/demux-qzv-interpretation-for-dada2-and-or-deblur/11896 "2019-10-17T02:09:25Z")
Hi, I've looked around on the forum for help with interpreting an interactive quality plot from demux.qzv that is close to mine, but I haven't found any similar situations. I'm using QIIME2 version 2019.1 through Virtu… --- ## [impact of quality primer on the quality of data](https://forum.qiime2.org/t/impact-of-quality-primer-on-the-quality-of-data/11858)
**Author:** [@Cravo\_Adri](https://forum.qiime2.org/u/Cravo_Adri)\ **Replies:** 2\ **Last updated:** [October 10, 2019, 12:40pm UTC](https://forum.qiime2.org/t/impact-of-quality-primer-on-the-quality-of-data/11858 "2019-10-10T12:40:59Z")
Hi, everyone, I searched in the forum and did not find the answer to my question, maybe you can help me. I'm sequencing my samples for both 16S and 18S, but they come from a vertebrate, so there was a lot of host seque… --- ## [Filtering with deblur](https://forum.qiime2.org/t/filtering-with-deblur/7912)
**Author:** [@kedi](https://forum.qiime2.org/u/kedi)\ **Replies:** 5\ **Last updated:** [January 22, 2019, 2:08pm UTC](https://forum.qiime2.org/t/filtering-with-deblur/7912 "2019-01-22T14:08:49Z")
qiime feature-table summarize --i-table table.qza --o-visualization table.qzv --m-sample-metadata-file F.metadata4.tsv error: Plugin error from feature-table: ids\_to\_keep must contain at least one ID., I'm certain tha… --- ## [Where to trim reads](https://forum.qiime2.org/t/where-to-trim-reads/5741)
**Author:** [@ariel](https://forum.qiime2.org/u/ariel)\ **Replies:** 24\ **Last updated:** [August 30, 2018, 1:05am UTC](https://forum.qiime2.org/t/where-to-trim-reads/5741 "2018-08-30T01:05:44Z")
Hello, thank you again for providing this resource and answering so many questions! I read a number of other questions on this topic, however I'm hoping that someone can sanity check my primer calculations and trimming. … --- ## [Recommendation for processing forward and reverse reads with low quality issues](https://forum.qiime2.org/t/recommendation-for-processing-forward-and-reverse-reads-with-low-quality-issues/3730)
**Author:** [@jorge\_rico](https://forum.qiime2.org/u/jorge_rico)\ **Replies:** 2\ **Last updated:** [May 7, 2018, 1:03pm UTC](https://forum.qiime2.org/t/recommendation-for-processing-forward-and-reverse-reads-with-low-quality-issues/3730 "2018-05-07T13:03:20Z")
Hi, I have a 16S rRNA amplicon data set (EMP standard primers) that was sequenced at a facility and the returned reads aren't great quality, especially the reverse reads. See screenshot and uploaded .qzv. My questions ar… --- ## [Interactive quality plot colors](https://forum.qiime2.org/t/interactive-quality-plot-colors/2990)
**Author:** [@Vixer](https://forum.qiime2.org/u/Vixer)\ **Replies:** 19\ **Last updated:** [April 30, 2018, 5:32pm UTC](https://forum.qiime2.org/t/interactive-quality-plot-colors/2990 "2018-04-30T17:32:33Z")
Hello, I´m enjoyin so far working with QIIME2, it´s just too good! I also have been reading about the quality plot in the forum and I noticed that my sequences have also red bars like the ones described in this post abo… --- ## [Low sequence counts](https://forum.qiime2.org/t/low-sequence-counts/3283)
**Author:** [@Jeongsu\_Kim](https://forum.qiime2.org/u/Jeongsu_Kim)\ **Replies:** 5\ **Last updated:** [March 5, 2018, 5:36pm UTC](https://forum.qiime2.org/t/low-sequence-counts/3283 "2018-03-05T17:36:04Z")
I looked into the file table.qzv to determine --p-sampling-depth for qiime diversity core-metrics-phylogenetic analysis. I found that sequence counts per samples are very low. I have 70 samples but the total counts is … --- ## [Raw quality data](https://forum.qiime2.org/t/raw-quality-data/1702)
**Author:** [@jacodela](https://forum.qiime2.org/u/jacodela)\ **Replies:** 2\ **Last updated:** [February 16, 2018, 4:08pm UTC](https://forum.qiime2.org/t/raw-quality-data/1702 "2018-02-16T16:08:33Z")
Hi, I'm trying to determine the adequate cutoff value for trimming my reads. I want to select this value in a way more objective than squinting at the boxplot in the visualization artifact, and I'd like to access the r… --- ## [Export demux interactive quality plots as csv](https://forum.qiime2.org/t/export-demux-interactive-quality-plots-as-csv/2431)
**Author:** [@mahermassoud](https://forum.qiime2.org/u/mahermassoud)\ **Replies:** 6\ **Last updated:** [February 16, 2018, 3:56pm UTC](https://forum.qiime2.org/t/export-demux-interactive-quality-plots-as-csv/2431 "2018-02-16T15:56:45Z")
I am interested in aggregating lots of the data used to make quality plots like this one (click "Interactive Quality Plot") to train an error model. When I click export csv, I do not get the quality data. Is there a way… --- ## [Interactive quality plot interpretation and colors](https://forum.qiime2.org/t/interactive-quality-plot-interpretation-and-colors/1843)
**Author:** [@Sarah\_McGrath](https://forum.qiime2.org/u/Sarah_McGrath)\ **Replies:** 4\ **Last updated:** [December 22, 2017, 5:59pm UTC](https://forum.qiime2.org/t/interactive-quality-plot-interpretation-and-colors/1843 "2017-12-22T17:59:52Z")
Hello, I am new to interpreting quality plots of my data and had a question about the interactive quality plots produced in qiime2. Below is a screen shot of the quality plot for my forward reads: Here is the file … --- ## [Quick viewer for Qiime 2 artifacts](https://forum.qiime2.org/t/quick-viewer-for-qiime-2-artifacts/2051)
**Author:** [@Gluque](https://forum.qiime2.org/u/Gluque)\ **Replies:** 2\ **Last updated:** [December 1, 2017, 9:00pm UTC](https://forum.qiime2.org/t/quick-viewer-for-qiime-2-artifacts/2051 "2017-12-01T21:00:59Z")
Hi there! For those who -like us- has several restrictions moving data out of our servers, here in our lab we have develop a tool called qiime\_2\_ll\_quick\_viewer which you can use to open your Qiime 2 visualization artif… --- ## [Strange quality patterns from seqmatic data that does not match FastQC quality scores](https://forum.qiime2.org/t/strange-quality-patterns-from-seqmatic-data-that-does-not-match-fastqc-quality-scores/1643)
**Author:** [@jessicalmetcalf](https://forum.qiime2.org/u/jessicalmetcalf)\ **Replies:** 1\ **Last updated:** [October 31, 2017, 7:36pm UTC](https://forum.qiime2.org/t/strange-quality-patterns-from-seqmatic-data-that-does-not-match-fastqc-quality-scores/1643 "2017-10-31T19:36:46Z")
Hello, two of my students have data sets that they are re-analyzing in qiime2. These 16S rRNA data sets (515f/806r) were generated by the company Seqmatic. Using FastQC, their quality appears fine for each sample. Howeve… --- ## [Finding Primers In Raw Files and Quality Control](https://forum.qiime2.org/t/finding-primers-in-raw-files-and-quality-control/1621)
**Author:** [@Pauline\_Trinh](https://forum.qiime2.org/u/Pauline_Trinh)\ **Replies:** 4\ **Last updated:** [October 27, 2017, 9:55pm UTC](https://forum.qiime2.org/t/finding-primers-in-raw-files-and-quality-control/1621 "2017-10-27T21:55:40Z")
I'm just switching over to QIIME2 and excited about using DADA2 but I'm a little confused about two things. I've inherited some fastq demultiplexed paired end files and I'm uncertain if the primers are still in these …