# \#truncate **URL:** https://forum.qiime2.org/tag/truncate/103.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Inadequate overlap for V3-V4 (paired-end) due to quality drop](https://forum.qiime2.org/t/inadequate-overlap-for-v3-v4-paired-end-due-to-quality-drop/34006)
**Author:** [@Gorka\_Garcia](https://forum.qiime2.org/u/Gorka_Garcia)\ **Replies:** 5\ **Last updated:** [March 9, 2026, 8:14pm UTC](https://forum.qiime2.org/t/inadequate-overlap-for-v3-v4-paired-end-due-to-quality-drop/34006 "2026-03-09T20:14:38Z")
Hi everyone, I am currently analyzing 16S rRNA gene sequences (V3-V4 region) using QIIME2. I am facing a challenge during the denoising step with dada2 denoise-paired. The problem is that my sequencing quality drops si… --- ## [Losing a lot of reads during merging](https://forum.qiime2.org/t/losing-a-lot-of-reads-during-merging/33021)
**Author:** [@Shinthotrang](https://forum.qiime2.org/u/Shinthotrang)\ **Replies:** 3\ **Last updated:** [April 18, 2025, 3:51pm UTC](https://forum.qiime2.org/t/losing-a-lot-of-reads-during-merging/33021 "2025-04-18T15:51:16Z")
Greetings. I'm new to QIIME2. So there are still a lot of things I need to learn and I appreciate all of helps I can receive. Currently, I'm conducting a 16s QIIME2 analysis pipeline based on moving picture tutorials to… --- ## [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… --- ## [Dada2, trunc len](https://forum.qiime2.org/t/dada2-trunc-len/28469)
**Author:** [@Linda\_Abenaim](https://forum.qiime2.org/u/Linda_Abenaim)\ **Replies:** 11\ **Last updated:** [December 1, 2023, 2:49pm UTC](https://forum.qiime2.org/t/dada2-trunc-len/28469 "2023-12-01T14:49:45Z")
Hello everyone! I followed a lot of previous topics on this forum, but I need some help on my denoising. here you can find my demux-summary demux-summary.qzv (320.5 KB) My sequencing is on gene 16s rRNA with amplific… --- ## [help for chosing a truncating parameter for dada2](https://forum.qiime2.org/t/help-for-chosing-a-truncating-parameter-for-dada2/26351)
**Author:** [@aymericola](https://forum.qiime2.org/u/aymericola)\ **Replies:** 2\ **Last updated:** [May 9, 2023, 8:45am UTC](https://forum.qiime2.org/t/help-for-chosing-a-truncating-parameter-for-dada2/26351 "2023-05-09T08:45:41Z")
Hello, I am struggling with finding the proper truncating parameter for dada2. For the moment, I've imported my data to Qiime2 (Casava1.8 format) and visualized them. The results are the following : In the resourc… --- ## [Interpretation of quality plots](https://forum.qiime2.org/t/interpretation-of-quality-plots/25733)
**Author:** [@Miri\_J](https://forum.qiime2.org/u/Miri_J)\ **Replies:** 9\ **Last updated:** [March 20, 2023, 9:27am UTC](https://forum.qiime2.org/t/interpretation-of-quality-plots/25733 "2023-03-20T09:27:51Z")
Hello, this is my first time using Qiime2. After looking at the different interactive quality plots made by other users, I am unsure whether mine looks correct or needs denoising. This is what my quality plot looks l… --- ## [deciding where to truncate](https://forum.qiime2.org/t/deciding-where-to-truncate/22662)
**Author:** [@Azospirillum871](https://forum.qiime2.org/u/Azospirillum871)\ **Replies:** 2\ **Last updated:** [April 10, 2022, 1:12am UTC](https://forum.qiime2.org/t/deciding-where-to-truncate/22662 "2022-04-10T01:12:21Z")
I have been trying to decide where to truncate and would value others input. I think I should truncate forward 280 and reverse 200 to keep the 50th (Median) quality score above 30. --- ## [Should we truncate or not?](https://forum.qiime2.org/t/should-we-truncate-or-not/22635)
**Author:** [@Danique](https://forum.qiime2.org/u/Danique)\ **Replies:** 1\ **Last updated:** [March 31, 2022, 10:54am UTC](https://forum.qiime2.org/t/should-we-truncate-or-not/22635 "2022-03-31T10:54:36Z")
Hello, We are preparing our data for dada2 and are unsure about whether or not to truncate. I realize that there are already a few topics about truncating in DADA2, but I have not yet found a situation comparable to ou… --- ## [Truncate length for V3-V4 sequencing in dada2 process](https://forum.qiime2.org/t/truncate-length-for-v3-v4-sequencing-in-dada2-process/22539)
**Author:** [@Muhammad\_Zeeshan\_Akr](https://forum.qiime2.org/u/Muhammad_Zeeshan_Akr)\ **Replies:** 0\ **Last updated:** [March 23, 2022, 10:05am UTC](https://forum.qiime2.org/t/truncate-length-for-v3-v4-sequencing-in-dada2-process/22539 "2022-03-23T10:05:59Z")
Hi all, sorry for this question, i know it might have asked so many times. I just want to get more insights into it. Please provide your inputs. Thanks in advance. I have sequencing data (2​:multiply:300) of V3-V4 regio… --- ## [Where should I truncate my forward and reverse reads?](https://forum.qiime2.org/t/where-should-i-truncate-my-forward-and-reverse-reads/21688)
**Author:** [@bkramer](https://forum.qiime2.org/u/bkramer)\ **Replies:** 8\ **Last updated:** [December 21, 2021, 3:05pm UTC](https://forum.qiime2.org/t/where-should-i-truncate-my-forward-and-reverse-reads/21688 "2021-12-21T15:05:44Z")
Hello, I'm having issues determining where I should truncate my forward and reverse reads prior to denoising using dada2. Based on the reads (see attached .qzv file), it would seem I'd have to truncate to regions where … --- ## [Nomenclature issue: trimming vs truncation](https://forum.qiime2.org/t/nomenclature-issue-trimming-vs-truncation/21101)
**Author:** [@vheidrich](https://forum.qiime2.org/u/vheidrich)\ **Replies:** 5\ **Last updated:** [October 28, 2021, 8:13pm UTC](https://forum.qiime2.org/t/nomenclature-issue-trimming-vs-truncation/21101 "2021-10-28T20:13:21Z")
Hi everyone, After chatting with a collaborator, I am now questioning a little bit my interpretation of the terms trimming and truncation. What's the difference between them to you? My interpretation is that trimming i… --- ## [Issue with my dad2 denoise-paired command script](https://forum.qiime2.org/t/issue-with-my-dad2-denoise-paired-command-script/20224)
**Author:** [@bkramer](https://forum.qiime2.org/u/bkramer)\ **Replies:** 4\ **Last updated:** [August 13, 2021, 1:35pm UTC](https://forum.qiime2.org/t/issue-with-my-dad2-denoise-paired-command-script/20224 "2021-08-13T13:35:15Z")
I tried to use the dada2 denoise-paired command in qiime2 in order to truncate the forward and reverse sequences of a single sample, both of which I had already removed the primers using the cutadapt trim-paired command.… --- ## [DADA2 error (same error for every try)](https://forum.qiime2.org/t/dada2-error-same-error-for-every-try/20335)
**Author:** [@hjpyun](https://forum.qiime2.org/u/hjpyun)\ **Replies:** 0\ **Last updated:** [July 29, 2021, 4:02pm UTC](https://forum.qiime2.org/t/dada2-error-same-error-for-every-try/20335 "2021-07-29T16:02:13Z")
Hi, everyone. I have some problems with qiime2 dada2 denoise-paired The thing is that the same error is coming up. I tried changing parameters (trunc, trim length) but same error is coming up. qiime dada2 denoise-pair… --- ## [DADA2 Quality Control ERROR](https://forum.qiime2.org/t/dada2-quality-control-error/18440)
**Author:** [@matthewbur](https://forum.qiime2.org/u/matthewbur)\ **Replies:** 1\ **Last updated:** [February 10, 2021, 7:25am UTC](https://forum.qiime2.org/t/dada2-quality-control-error/18440 "2021-02-10T07:25:43Z")
Hello. I am currently using Qiime2-2020.11 and began receiving an error during my quality control step for the first time. Code: qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trim-left-f 19 --p-… --- ## [dada2 paired end denoising max overlapping base](https://forum.qiime2.org/t/dada2-paired-end-denoising-max-overlapping-base/12276)
**Author:** [@the\_dummy](https://forum.qiime2.org/u/the_dummy)\ **Replies:** 2\ **Last updated:** [November 1, 2019, 10:11am UTC](https://forum.qiime2.org/t/dada2-paired-end-denoising-max-overlapping-base/12276 "2019-11-01T10:11:56Z")
I know that we should use 30 overlapping bases at least. But, I don't know about if there is a maximum. I have 2x250 paired end data and quality scores for all positions are over 25, so I'm not sure if I should truncate … --- ## [Need a second opinion on my data - DADA2, truncation length for V4 region - 250 bases PE read data](https://forum.qiime2.org/t/need-a-second-opinion-on-my-data-dada2-truncation-length-for-v4-region-250-bases-pe-read-data/4401)
**Author:** [@anwesh](https://forum.qiime2.org/u/anwesh)\ **Replies:** 1\ **Last updated:** [June 4, 2018, 10:42pm UTC](https://forum.qiime2.org/t/need-a-second-opinion-on-my-data-dada2-truncation-length-for-v4-region-250-bases-pe-read-data/4401 "2018-06-04T22:42:17Z")
Hi all, I know this question has been asked earlier, but I just want to confirm that I'm doing it right for my dataset, so, please input your suggestions... Here are the details and workflow... Dataset Properties: 7 s… --- ## [Can anyone help me in truncating sequences with qiime dada2 denoise-paired \\?](https://forum.qiime2.org/t/can-anyone-help-me-in-truncating-sequences-with-qiime-dada2-denoise-paired/4366)
**Author:** [@Aqleem12](https://forum.qiime2.org/u/Aqleem12)\ **Replies:** 3\ **Last updated:** [June 1, 2018, 3:36am UTC](https://forum.qiime2.org/t/can-anyone-help-me-in-truncating-sequences-with-qiime-dada2-denoise-paired/4366 "2018-06-01T03:36:04Z")
Dear All, After getting demux.qzv file and viewing the sequence quality at https://view.qiime2.org. I tried to cut the sequences using the following message: Qiime-dada2 denoise-paired --i-demultiplexed-seqs aqleem12… --- ## [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… --- ## [DADA2 features and frequencies](https://forum.qiime2.org/t/dada2-features-and-frequencies/3043)
**Author:** [@asr17](https://forum.qiime2.org/u/asr17)\ **Replies:** 8\ **Last updated:** [February 16, 2018, 1:18am UTC](https://forum.qiime2.org/t/dada2-features-and-frequencies/3043 "2018-02-16T01:18:05Z")
Hi experts, I am trying to figure out the best settings in DADA2 on my MiSeq PE reads targeting ITS2. In a previous post I found it very helpful, the focus was mainly on the number of features in setting trunc-len DADA2… --- ## [What should be the best trim and truncate length size](https://forum.qiime2.org/t/what-should-be-the-best-trim-and-truncate-length-size/2019)
**Author:** [@drmusk](https://forum.qiime2.org/u/drmusk)\ **Replies:** 1\ **Last updated:** [November 30, 2017, 2:24pm UTC](https://forum.qiime2.org/t/what-should-be-the-best-trim-and-truncate-length-size/2019 "2017-11-30T14:24:52Z")
Dear Colleagues For the image below of interactive quality what should be ideal trim and truncate. I personally think --p-trim-left-f 17 --p-trim-left-r 0 --p-trunc-len-f 105 --p-trunc-len-r 28 --- ## [I donot know how to truncate paired sequence bases. How do we know about the quality of the bases is high or low?](https://forum.qiime2.org/t/i-donot-know-how-to-truncate-paired-sequence-bases-how-do-we-know-about-the-quality-of-the-bases-is-high-or-low/1437)
**Author:** [@Aqleem12](https://forum.qiime2.org/u/Aqleem12)\ **Replies:** 3\ **Last updated:** [October 10, 2017, 7:13pm UTC](https://forum.qiime2.org/t/i-donot-know-how-to-truncate-paired-sequence-bases-how-do-we-know-about-the-quality-of-the-bases-is-high-or-low/1437 "2017-10-10T19:13:00Z")
In the demux.qzv quality plots, i.e . two quality plots one for forward and one for reverse. I donot know how to truncated both quality plots. I have attached the file. Please help me in sequence quality control I used …