# \#deblur **URL:** https://forum.qiime2.org/tag/deblur/12.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Under the hood of the "Moving Pictures" tutorial](https://forum.qiime2.org/t/under-the-hood-of-the-moving-pictures-tutorial/34173)
**Author:** [@Phi\_Nguyen](https://forum.qiime2.org/u/Phi_Nguyen)\ **Replies:** 0\ **Last updated:** [May 13, 2026, 6:27pm UTC](https://forum.qiime2.org/t/under-the-hood-of-the-moving-pictures-tutorial/34173 "2026-05-13T18:27:41Z")
Hi QIIME 2 Community, I am a bioinformatician who has been working closely with QIIME 2. I’ve noticed that while the "Moving Pictures" tutorial is the gold standard for gaining initial experience, many newcomers struggl… --- ## [High read loss due to artifacts and chimera after denoising 16S V3-V4 paired-end reads](https://forum.qiime2.org/t/high-read-loss-due-to-artifacts-and-chimera-after-denoising-16s-v3-v4-paired-end-reads/33870)
**Author:** [@Saif\_Arosh](https://forum.qiime2.org/u/Saif_Arosh)\ **Replies:** 1\ **Last updated:** [December 17, 2025, 3:14pm UTC](https://forum.qiime2.org/t/high-read-loss-due-to-artifacts-and-chimera-after-denoising-16s-v3-v4-paired-end-reads/33870 "2025-12-17T15:14:07Z")
Hello Everyone, So, I have successfully denoised my 16S V3–V4 paired-end reads from stool samples, my forward reads (FRs) are all high quality (median score 40) at upto 301bp length, but my reverse reads show poor quali… --- ## [High read loss after Deblur denoise-other despite permissive parameters and mostly uniform-length reads](https://forum.qiime2.org/t/high-read-loss-after-deblur-denoise-other-despite-permissive-parameters-and-mostly-uniform-length-reads/33728)
**Author:** [@Shashi.Kiran](https://forum.qiime2.org/u/Shashi.Kiran)\ **Replies:** 1\ **Last updated:** [October 20, 2025, 9:16pm UTC](https://forum.qiime2.org/t/high-read-loss-after-deblur-denoise-other-despite-permissive-parameters-and-mostly-uniform-length-reads/33728 "2025-10-20T21:16:03Z")
Hello QIIME2 team, I am running Deblur with the following command using QIIME2 (2024.5): qiime deblur denoise-other --i-demultiplexed-seqs reads\_qza/reads\_trimmed\_joined.qza --i-reference-seqs ref\_seq.qza --p-trim-l… --- ## [How to Analyzing Multi-Run Sequencing Data in QIIME2 with Minimal Batch Effects](https://forum.qiime2.org/t/how-to-analyzing-multi-run-sequencing-data-in-qiime2-with-minimal-batch-effects/32641)
**Author:** [@Brandon](https://forum.qiime2.org/u/Brandon)\ **Replies:** 6\ **Last updated:** [February 27, 2025, 7:05pm UTC](https://forum.qiime2.org/t/how-to-analyzing-multi-run-sequencing-data-in-qiime2-with-minimal-batch-effects/32641 "2025-02-27T19:05:07Z")
Hi QIIME2 experts, I have datasets from three sequencing runs: One from an Illumina MiSeq machine One from an Illumina NextSeq machine One from an older version of the Illumina MiSeq machine All datasets consist of p… --- ## [Issues with Denoising Using DADA2 and Deblur - Parameter Tuning and Merging Sequences](https://forum.qiime2.org/t/issues-with-denoising-using-dada2-and-deblur-parameter-tuning-and-merging-sequences/31991)
**Author:** [@Siqin\_Zhang](https://forum.qiime2.org/u/Siqin_Zhang)\ **Replies:** 1\ **Last updated:** [December 2, 2024, 6:35pm UTC](https://forum.qiime2.org/t/issues-with-denoising-using-dada2-and-deblur-parameter-tuning-and-merging-sequences/31991 "2024-12-02T18:35:55Z")
Hi everyone, I am sorry for the long post, but I wanted to provide as much detail as possible. I am new to using QIIME 2 - 2024.2 (miniconda3) and I have sequences from a 2 x 300 bp Illumina run (338F\_806R). Attached a… --- ## [Deblur Denoise Plugin Error Message](https://forum.qiime2.org/t/deblur-denoise-plugin-error-message/31934)
**Author:** [@jakeroush4](https://forum.qiime2.org/u/jakeroush4)\ **Replies:** 1\ **Last updated:** [November 19, 2024, 5:14pm UTC](https://forum.qiime2.org/t/deblur-denoise-plugin-error-message/31934 "2024-11-19T17:14:16Z")
Hello- I am running qiime2-amplicon-2024.5 I am trying to run deblur denoise on CO1 sequence data and continue to get this error message "Plugin error from deblur: Command '\['deblur', 'workflow', '--seqs-fp', '/tmp/qi… --- ## [what is the best application strategy for analyzing large scale dataset](https://forum.qiime2.org/t/what-is-the-best-application-strategy-for-analyzing-large-scale-dataset/31709)
**Author:** [@Brandon](https://forum.qiime2.org/u/Brandon)\ **Replies:** 4\ **Last updated:** [October 25, 2024, 11:21pm UTC](https://forum.qiime2.org/t/what-is-the-best-application-strategy-for-analyzing-large-scale-dataset/31709 "2024-10-25T23:21:21Z")
Hi QIIME2 team, I am planning to analyze a large-scale dataset with over 10,000 samples, all of which are paired-end 16S data from different sequencing batches. The sequencing quality varies between batches, with some s… --- ## [Deblur usage for truncation from the end of the read](https://forum.qiime2.org/t/deblur-usage-for-truncation-from-the-end-of-the-read/31528)
**Author:** [@Pratyusha\_Patidar](https://forum.qiime2.org/u/Pratyusha_Patidar)\ **Replies:** 1\ **Last updated:** [September 27, 2024, 2:30pm UTC](https://forum.qiime2.org/t/deblur-usage-for-truncation-from-the-end-of-the-read/31528 "2024-09-27T14:30:08Z")
Can I use Deblur to remove the last 3 nts of my single end data? For instance, the total read lengh is 260 and I need to remove the bases from 258, 259, and 260 positions. I could only find "trim" option and not "trunc" … --- ## [Issues with Deblur and SortMeRNA](https://forum.qiime2.org/t/issues-with-deblur-and-sortmerna/31308)
**Author:** [@ricknematodeguy](https://forum.qiime2.org/u/ricknematodeguy)\ **Replies:** 2\ **Last updated:** [September 23, 2024, 6:28pm UTC](https://forum.qiime2.org/t/issues-with-deblur-and-sortmerna/31308 "2024-09-23T18:28:58Z")
Hello there! I have run into an issue with denoising after merging reads and quality filter. The issue seems to be some issue with SortMeRNA, though I'm not sure what. Here is the code I ran for the denoising: nohup q… --- ## [importing data failed](https://forum.qiime2.org/t/importing-data-failed/30699)
**Author:** [@freedom\_0079](https://forum.qiime2.org/u/freedom_0079)\ **Replies:** 5\ **Last updated:** [July 8, 2024, 5:19pm UTC](https://forum.qiime2.org/t/importing-data-failed/30699 "2024-07-08T17:19:29Z")
hello, I am trying to run deblur single sequence, I convert all my file to fastq, removed the primer and made manifest file. when I try to import the files : iime tools import \\ --input-path /Users/freedom/Desktop/ch… --- ## [Potential artifacts produced with DADA2 wrapped in qiime2-2018.8 - need advice](https://forum.qiime2.org/t/potential-artifacts-produced-with-dada2-wrapped-in-qiime2-2018-8-need-advice/7318)
**Author:** [@jcmcnch](https://forum.qiime2.org/u/jcmcnch)\ **Replies:** 6\ **Last updated:** [January 7, 2019, 3:14am UTC](https://forum.qiime2.org/t/potential-artifacts-produced-with-dada2-wrapped-in-qiime2-2018-8-need-advice/7318 "2019-01-07T03:14:46Z")
Hi folks, My name's Jesse, and I'm working in Jed Fuhrman's lab at USC. My colleague Yi-Chun (@LivYeh) and I have been developing a protocol for qiime2 for analyzing the mixed 16s/18s amplicons that are produced by the 5… --- ## [Why does deblur denoise lead to the removal of the complete removal of the larger samples](https://forum.qiime2.org/t/why-does-deblur-denoise-lead-to-the-removal-of-the-complete-removal-of-the-larger-samples/30335)
**Author:** [@KpatelBio](https://forum.qiime2.org/u/KpatelBio)\ **Replies:** 1\ **Last updated:** [June 4, 2024, 12:12am UTC](https://forum.qiime2.org/t/why-does-deblur-denoise-lead-to-the-removal-of-the-complete-removal-of-the-larger-samples/30335 "2024-06-04T00:12:47Z")
Dear qiime forum, I am finding that use of deblur denoise might be too powerful for my dataset, as almost 99% of the input number of reads end up being removed. Reads per sample after q-score removal (column reads-raw… --- ## [Dada2 or Deblur](https://forum.qiime2.org/t/dada2-or-deblur/30230)
**Author:** [@Achraf\_Zbaida](https://forum.qiime2.org/u/Achraf_Zbaida)\ **Replies:** 2\ **Last updated:** [May 16, 2024, 5:03pm UTC](https://forum.qiime2.org/t/dada2-or-deblur/30230 "2024-05-16T17:03:34Z")
I want to use DADA2 or Deblur to generate FeatureData\[Sequence\] and FeatureTable\[Frequency\] , but both commands are not working. DADA2 : qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trim-left … --- ## [Error during deblur process](https://forum.qiime2.org/t/error-during-deblur-process/29756)
**Author:** [@moshhoss](https://forum.qiime2.org/u/moshhoss)\ **Replies:** 7\ **Last updated:** [May 11, 2024, 9:03pm UTC](https://forum.qiime2.org/t/error-during-deblur-process/29756 "2024-05-11T21:03:07Z")
Hello everyone! I am new to doing bioinformatics stuff. I have little to no background on it and I am assigned to help a professor do some taxonomic analysis. I installed QIIME2 v2024.2 amplicon. FASTQ files are from Ame… --- ## [How to choose a reasonable trim-length for Deblur plugin?](https://forum.qiime2.org/t/how-to-choose-a-reasonable-trim-length-for-deblur-plugin/30003)
**Author:** [@peccat](https://forum.qiime2.org/u/peccat)\ **Replies:** 5\ **Last updated:** [April 24, 2024, 3:03am UTC](https://forum.qiime2.org/t/how-to-choose-a-reasonable-trim-length-for-deblur-plugin/30003 "2024-04-24T03:03:04Z")
Hey everyone, Happy to post my first topic, as a new member joining the big family of Qiime2 forum. Recently I taught myself the knowledge of denoising protocols, and several problems in terms of reads truncation and t… --- ## [Issues during denoising with NextSeq 16S data.](https://forum.qiime2.org/t/issues-during-denoising-with-nextseq-16s-data/27584)
**Author:** [@eoinoh91](https://forum.qiime2.org/u/eoinoh91)\ **Replies:** 1\ **Last updated:** [September 7, 2023, 8:04am UTC](https://forum.qiime2.org/t/issues-during-denoising-with-nextseq-16s-data/27584 "2023-09-07T08:04:38Z")
Hi all, I've run into an issue with NextSeq data in QIIME2, in that we are losing 75%+ of the sequences during the DADA2 denoising step. We have 2x300bp sequencing data for the V3-V4 16S region, amplified with the … --- ## [deblur denoise-16S PACBIO](https://forum.qiime2.org/t/deblur-denoise-16s-pacbio/27386)
**Author:** [@coder](https://forum.qiime2.org/u/coder)\ **Replies:** 1\ **Last updated:** [August 15, 2023, 2:19pm UTC](https://forum.qiime2.org/t/deblur-denoise-16s-pacbio/27386 "2023-08-15T14:19:44Z")
environment : qiime2 2023.05 - docker-image data:PACBIO sequel II my command as follows: qiime tools import --type 'SampleData\[SequencesWithQuality\]' --input-path ../input-path-list.tsv … --- ## [deblur denoise-other ITS error](https://forum.qiime2.org/t/deblur-denoise-other-its-error/27321)
**Author:** [@Rachel\_Burke](https://forum.qiime2.org/u/Rachel_Burke)\ **Replies:** 7\ **Last updated:** [August 9, 2023, 4:15pm UTC](https://forum.qiime2.org/t/deblur-denoise-other-its-error/27321 "2023-08-09T16:15:02Z")
I am having issues with deblur denoise-other for assembling ITS. I used the UNITE database--specifically the "Includes singletons set as RefS (in dynamic files)" one, and only used the dynamic file (not 99 or 97) for the… --- ## [Deciding trim length for deblur](https://forum.qiime2.org/t/deciding-trim-length-for-deblur/27260)
**Author:** [@mjais](https://forum.qiime2.org/u/mjais)\ **Replies:** 2\ **Last updated:** [July 31, 2023, 7:16pm UTC](https://forum.qiime2.org/t/deciding-trim-length-for-deblur/27260 "2023-07-31T19:16:18Z")
Hi, I have 10 samples paired-end data and after importing it, I merged it by using vsearch merge-pairs. Then applied quality control to the sequences using quality-filter q-score. After that, I am proceeding with the de… --- ## [Deblur multiple sequencing alignment (MSA) failed by message "may be only 1 read?"](https://forum.qiime2.org/t/deblur-multiple-sequencing-alignment-msa-failed-by-message-may-be-only-1-read/26975)
**Author:** [@deepak](https://forum.qiime2.org/u/deepak)\ **Replies:** 8\ **Last updated:** [July 10, 2023, 6:57pm UTC](https://forum.qiime2.org/t/deblur-multiple-sequencing-alignment-msa-failed-by-message-may-be-only-1-read/26975 "2023-07-10T18:57:08Z")
Hi I am using Deblur denoise for 32 samples. At denoising step analysis failed at MSA and showing message "msa failed for file/xyz .fastq.gz.trim.derep.no\_artifacts (maybe only 1 read?)". In the same log file, it shows… --- ## [Sample files need to have underscores to be imported but Sample IDs cannot have underscores for deblur](https://forum.qiime2.org/t/sample-files-need-to-have-underscores-to-be-imported-but-sample-ids-cannot-have-underscores-for-deblur/26272)
**Author:** [@mcmk3](https://forum.qiime2.org/u/mcmk3)\ **Replies:** 1\ **Last updated:** [May 1, 2023, 5:56pm UTC](https://forum.qiime2.org/t/sample-files-need-to-have-underscores-to-be-imported-but-sample-ids-cannot-have-underscores-for-deblur/26272 "2023-05-01T17:56:46Z")
Hi, I am importing sequence files of the input-format CasavaOneEightSingleLanePerSampleDirFmt (see below). These are required to be named in the following format for import: '.+\_.+\_L\[0-9\]\[0-9\]\[0-9\]\_R\[12\]\_001\\.fastq\\.gz… --- ## [Deblur error with 16S from Novaseq data](https://forum.qiime2.org/t/deblur-error-with-16s-from-novaseq-data/25941)
**Author:** [@AMosca96](https://forum.qiime2.org/u/AMosca96)\ **Replies:** 3\ **Last updated:** [April 3, 2023, 3:50pm UTC](https://forum.qiime2.org/t/deblur-error-with-16s-from-novaseq-data/25941 "2023-04-03T15:50:41Z")
Hi everyone, I am using deblur through QIIME2-2022.8 for 16S data (v3-v4 regions) and I saw many posts about this error message from deblur but, as far I could see, not related to NovaSeq data.: No sequences passed th… --- ## [Good classification, poor clustering](https://forum.qiime2.org/t/good-classification-poor-clustering/25771)
**Author:** [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)\ **Replies:** 2\ **Last updated:** [March 13, 2023, 7:38pm UTC](https://forum.qiime2.org/t/good-classification-poor-clustering/25771 "2023-03-13T19:38:16Z")
Hi Team! I've got a weird conundrum, and I'm hoping for some hive mind wisdom. I've got a data set that is 16S V34 Illumina paired end data and I'm running in qiime2-2022.2. Because of several project related constrain… --- ## [LOW percentage of input merged](https://forum.qiime2.org/t/low-percentage-of-input-merged/25590)
**Author:** [@aprillee826](https://forum.qiime2.org/u/aprillee826)\ **Replies:** 4\ **Last updated:** [February 24, 2023, 10:20am UTC](https://forum.qiime2.org/t/low-percentage-of-input-merged/25590 "2023-02-24T10:20:08Z")
Hi everyone, I would like to ask why the splicing rate between the left and right ends of my data is only 1%, and what are the possible reasons for this result? (Experimental and raw letter analysis) And how can we impro… --- ## [Quality Filtering using Deblur Error](https://forum.qiime2.org/t/quality-filtering-using-deblur-error/25281)
**Author:** [@irvinng98](https://forum.qiime2.org/u/irvinng98)\ **Replies:** 9\ **Last updated:** [January 25, 2023, 10:06pm UTC](https://forum.qiime2.org/t/quality-filtering-using-deblur-error/25281 "2023-01-25T22:06:36Z")
Hello, I'm trying to do quality filtering using the deblur method. However, when I run the qiime quality-filter q-score function, I get an error (see below). - Version of QIIME 2 you are running, and how it is installe… --- ## [Deblur Format Specifications](https://forum.qiime2.org/t/deblur-format-specifications/25252)
**Author:** [@Taylorr](https://forum.qiime2.org/u/Taylorr)\ **Replies:** 1\ **Last updated:** [January 23, 2023, 3:55pm UTC](https://forum.qiime2.org/t/deblur-format-specifications/25252 "2023-01-23T15:55:29Z")
Hello! So I am interested in trying the deblur plug-in to process my sequencing data; however, in the past, I have struggled with formatting issues. For instance, it seems that Deblur does not accept file names with und… --- ## [Finding the deblur log for API interface](https://forum.qiime2.org/t/finding-the-deblur-log-for-api-interface/25016)
**Author:** [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)\ **Replies:** 1\ **Last updated:** [December 15, 2022, 4:46pm UTC](https://forum.qiime2.org/t/finding-the-deblur-log-for-api-interface/25016 "2022-12-15T16:46:58Z")
Hi all! I've got data that for reasons:tm: needs to be denoised with deblur. (Mostly I dont know about the pre-processing or sequencing run batches). I'm entering debluring with like 20,000 reads before quality filterin… --- ## [p trim length deblur](https://forum.qiime2.org/t/p-trim-length-deblur/24947)
**Author:** [@bhaan](https://forum.qiime2.org/u/bhaan)\ **Replies:** 1\ **Last updated:** [December 8, 2022, 10:35pm UTC](https://forum.qiime2.org/t/p-trim-length-deblur/24947 "2022-12-08T22:35:39Z")
Hi everyone, I am very new to qiime2 and was wondering if someone could help me with choosing a p-trim length for good-quality reads as I am struggling to do so. I know it should be greater than 300 but I am unsure wher… --- ## [Moving Pictures Tutorial Hang-up...](https://forum.qiime2.org/t/moving-pictures-tutorial-hang-up/24615)
**Author:** [@Taylorr](https://forum.qiime2.org/u/Taylorr)\ **Replies:** 6\ **Last updated:** [November 16, 2022, 10:56pm UTC](https://forum.qiime2.org/t/moving-pictures-tutorial-hang-up/24615 "2022-11-16T22:56:11Z")
Hello! So I am testing out the Moving Pictures Tutorial to familiarise myself with qiime2 and deblur. However, I am running into issues importing my data: I am able to download the barcodes, but I get this response when… --- ## [demux command compatibility](https://forum.qiime2.org/t/demux-command-compatibility/24685)
**Author:** [@Taylorr](https://forum.qiime2.org/u/Taylorr)\ **Replies:** 1\ **Last updated:** [November 16, 2022, 7:35pm UTC](https://forum.qiime2.org/t/demux-command-compatibility/24685 "2022-11-16T19:35:21Z")
Hello! I am attempting to demultiplex my data with demux but I am unsure how to have this command read my files properly. My sequences are in .fastq format and my mapping file is just a .txt and looks like this: Doe… [Next page](https://forum.qiime2.org/tag/deblur/12.md?match_all_tags=true&page=1&tags%5B%5D=deblur)