# \#merge **URL:** https://forum.qiime2.org/tag/merge/74.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Query about false read merging or no read merging](https://forum.qiime2.org/t/query-about-false-read-merging-or-no-read-merging/34189)
**Author:** [@ahsankaleem](https://forum.qiime2.org/u/ahsankaleem)\ **Replies:** 1\ **Last updated:** [May 26, 2026, 6:59am UTC](https://forum.qiime2.org/t/query-about-false-read-merging-or-no-read-merging/34189 "2026-05-26T06:59:07Z")
Hello everyone! I hope that you are well. I have performed 2x250 bp paired-end sequencing of the V4-V5 region using a V2 500-cycle kit (7.5pM library with 20% PhiX). I got a cluster density of 1100K/mm², and a cluster p… --- ## [Significant 16S sequence loss while merging w/ DADA2, various truncation settings used](https://forum.qiime2.org/t/significant-16s-sequence-loss-while-merging-w-dada2-various-truncation-settings-used/33755)
**Author:** [@dmalcolm](https://forum.qiime2.org/u/dmalcolm)\ **Replies:** 2\ **Last updated:** [November 5, 2025, 5:00pm UTC](https://forum.qiime2.org/t/significant-16s-sequence-loss-while-merging-w-dada2-various-truncation-settings-used/33755 "2025-11-05T17:00:48Z")
Hello! This is my first post to the forum and, though it seems like a well-documented issue, I’ve had trouble finding a solution on my own using the previous topics and would greatly appreciate you all’s expertise and … --- ## [Recommended Step for Merging Metagenomics Datasets](https://forum.qiime2.org/t/recommended-step-for-merging-metagenomics-datasets/33448)
**Author:** [@charlesalexandreroy](https://forum.qiime2.org/u/charlesalexandreroy)\ **Replies:** 1\ **Last updated:** [July 16, 2025, 6:37am UTC](https://forum.qiime2.org/t/recommended-step-for-merging-metagenomics-datasets/33448 "2025-07-16T06:37:29Z")
Hi all, When merging multiple datasets, I know that for 16S data, it's recommended to denoise each run separately and then merge your feature tables. I'm wondering what the recommendation is for metagenomics data? Per t… --- ## [Duplicates causing issues, how to handle merging and clustering?](https://forum.qiime2.org/t/duplicates-causing-issues-how-to-handle-merging-and-clustering/30773)
**Author:** [@raivo-otus](https://forum.qiime2.org/u/raivo-otus)\ **Replies:** 2\ **Last updated:** [July 10, 2024, 8:18am UTC](https://forum.qiime2.org/t/duplicates-causing-issues-how-to-handle-merging-and-clustering/30773 "2024-07-10T08:18:16Z")
Hey, I am running qiime2 version 2024.2-amplicon. Background: I have single-end sequencing data of the ITS region. The data is from 11 separate runs, meaning I have 11 files of multiplexed sequences. There are replica… --- ## [Patterns in merging using DADA2](https://forum.qiime2.org/t/patterns-in-merging-using-dada2/29900)
**Author:** [@Tremadorr](https://forum.qiime2.org/u/Tremadorr)\ **Replies:** 8\ **Last updated:** [June 13, 2024, 2:06pm UTC](https://forum.qiime2.org/t/patterns-in-merging-using-dada2/29900 "2024-06-13T14:06:37Z")
Hi there! I have a 16S V3-4 (Klindworth) metabarcoding sequencing run from a study looking at freeze-thaw cycles across a fish farm impact gradient that is merging strangely. Essentially the further from the fish farm t… --- ## [issue with input to feature-table merge-seqs](https://forum.qiime2.org/t/issue-with-input-to-feature-table-merge-seqs/30275)
**Author:** [@op9183](https://forum.qiime2.org/u/op9183)\ **Replies:** 2\ **Last updated:** [May 20, 2024, 8:05pm UTC](https://forum.qiime2.org/t/issue-with-input-to-feature-table-merge-seqs/30275 "2024-05-20T20:05:37Z")
Hi all! Issue merging my data, code is as such: qiime feature-table merge-seqs --i-data rep-seqs-1.qza rep-seqs-2.qza --o-merged-data merged-reps.qza i've also tried splitting the inputs: qiime feature-table merg… --- ## [Understanding DADA2 parameters](https://forum.qiime2.org/t/understanding-dada2-parameters/29288)
**Author:** [@Anisur\_Rahman](https://forum.qiime2.org/u/Anisur_Rahman)\ **Replies:** 0\ **Last updated:** [February 17, 2024, 8:09pm UTC](https://forum.qiime2.org/t/understanding-dada2-parameters/29288 "2024-02-17T20:09:31Z")
Hi, I am a QIIME2 user. Currently, I am making some educational content on microbiome analysis mainly focusing on QIIME2. I found it always confusing to choose DADA2 parameters. And there are a lot of questions in the q… --- ## [Multiple lane runs on MiSeq of the same samples to get deeper sequencing depth. How to combine?](https://forum.qiime2.org/t/multiple-lane-runs-on-miseq-of-the-same-samples-to-get-deeper-sequencing-depth-how-to-combine/29132)
**Author:** [@Bark9299](https://forum.qiime2.org/u/Bark9299)\ **Replies:** 1\ **Last updated:** [February 2, 2024, 4:35pm UTC](https://forum.qiime2.org/t/multiple-lane-runs-on-miseq-of-the-same-samples-to-get-deeper-sequencing-depth-how-to-combine/29132 "2024-02-02T16:35:54Z")
Hello, I am somewhat new to bioinformatics and qiime2. I 16S sequenced 243 samples over 3 MiSeq lanes and now have 3x reverse and forward reads (paired end) for each sample. The goal of sequencing the same samples over 3… --- ## [DADA2, merging and overlap](https://forum.qiime2.org/t/dada2-merging-and-overlap/29043)
**Author:** [@stephhhhanniee](https://forum.qiime2.org/u/stephhhhanniee)\ **Replies:** 2\ **Last updated:** [January 26, 2024, 6:04pm UTC](https://forum.qiime2.org/t/dada2-merging-and-overlap/29043 "2024-01-26T18:04:06Z")
Hi everyone! I'm currently processing paired reads for 16S of V3-V4, forward (341F) and reverse (806R), with DADA2 and I was wondering if someone could help explain or confirm what I'm seeing in my results? My forward … --- ## [Looking for advice on poor merging results with vsearch](https://forum.qiime2.org/t/looking-for-advice-on-poor-merging-results-with-vsearch/27927)
**Author:** [@tamardigrade](https://forum.qiime2.org/u/tamardigrade)\ **Replies:** 9\ **Last updated:** [October 19, 2023, 5:02pm UTC](https://forum.qiime2.org/t/looking-for-advice-on-poor-merging-results-with-vsearch/27927 "2023-10-19T17:02:36Z")
Hi, I am having poor merging results with vsearch in QIIME and after trying a few things I found on this forum that didnt really change anything I figured I'd reach out for advice via post. Any suggestions on how to boo… --- ## [maximum mismatch by default at merge step between reverse and forward sequences](https://forum.qiime2.org/t/maximum-mismatch-by-default-at-merge-step-between-reverse-and-forward-sequences/27855)
**Author:** [@arthurs](https://forum.qiime2.org/u/arthurs)\ **Replies:** 1\ **Last updated:** [October 4, 2023, 5:26pm UTC](https://forum.qiime2.org/t/maximum-mismatch-by-default-at-merge-step-between-reverse-and-forward-sequences/27855 "2023-10-04T17:26:20Z")
Hello everyone, I am currently using QIIME 2 (version: 2023.7) to analyze an amplified gene with primers targeting the V4-V5 region of the small subunit of 16s rRNA in prokaryotes. I'm at the dada2 step and have a ques… --- ## [Low merged percentage with running DADA2](https://forum.qiime2.org/t/low-merged-percentage-with-running-dada2/27694)
**Author:** [@jazzy1](https://forum.qiime2.org/u/jazzy1)\ **Replies:** 8\ **Last updated:** [September 21, 2023, 11:43am UTC](https://forum.qiime2.org/t/low-merged-percentage-with-running-dada2/27694 "2023-09-21T11:43:21Z")
Hello, I am working with sequences generated on an Illumina MiSeq with v3 chemistry (2x300 bp) with primers targeting the V3/V4 region. The primers used were 341F (CCTACGGGNGGCWGCAG) and 805R (GACTACHVGGGTATCTAATCC). Bu… --- ## [Merge denoised table and sequence after denoised by deblur](https://forum.qiime2.org/t/merge-denoised-table-and-sequence-after-denoised-by-deblur/27641)
**Author:** [@turtle](https://forum.qiime2.org/u/turtle)\ **Replies:** 7\ **Last updated:** [September 13, 2023, 8:56pm UTC](https://forum.qiime2.org/t/merge-denoised-table-and-sequence-after-denoised-by-deblur/27641 "2023-09-13T20:56:05Z")
I have some confusion. I have to sequence files. Both are pair-end reads. But one of them has a very poor reverse read quality. So I decided to merge pair ends for the good one and then denoise it by deblur at 250 sequen… --- ## [merging sequence runs with slight primer variation](https://forum.qiime2.org/t/merging-sequence-runs-with-slight-primer-variation/27142)
**Author:** [@spongebob](https://forum.qiime2.org/u/spongebob)\ **Replies:** 8\ **Last updated:** [August 15, 2023, 2:32pm UTC](https://forum.qiime2.org/t/merging-sequence-runs-with-slight-primer-variation/27142 "2023-08-15T14:32:39Z")
Hi all, initial analysis done with qiime version: qiime2-2019.10 I have two data sets of 18S rRNA gene sequences from different sequence providers. The only difference is the reverse primer has an extra trailing TGA D… --- ## [meta-analysis using different sequencing platforms](https://forum.qiime2.org/t/meta-analysis-using-different-sequencing-platforms/27298)
**Author:** [@sudhir19](https://forum.qiime2.org/u/sudhir19)\ **Replies:** 1\ **Last updated:** [August 8, 2023, 8:49pm UTC](https://forum.qiime2.org/t/meta-analysis-using-different-sequencing-platforms/27298 "2023-08-08T20:49:43Z")
Hi everyone, I wanted to use data from studies using ion-torrent and Illumina platforms for a meta-analysis. Any thoughts on that, is it advisable, what are the things I should keep in mind if attempting anything like t… --- ## [Dada2 Merging Issue](https://forum.qiime2.org/t/dada2-merging-issue/27216)
**Author:** [@elmo2420](https://forum.qiime2.org/u/elmo2420)\ **Replies:** 3\ **Last updated:** [July 27, 2023, 11:23am UTC](https://forum.qiime2.org/t/dada2-merging-issue/27216 "2023-07-27T11:23:06Z")
My sequences aren't merging and I'm not sure where I am going wrong. For my parameters, I am trying to stay within 140-180 (forward) and 200-215(reverse) positions to be able to achieve an 80% for the input passed filter… --- ## [Failed in Reads merging](https://forum.qiime2.org/t/failed-in-reads-merging/26952)
**Author:** [@Rishikesh12](https://forum.qiime2.org/u/Rishikesh12)\ **Replies:** 5\ **Last updated:** [July 6, 2023, 1:37pm UTC](https://forum.qiime2.org/t/failed-in-reads-merging/26952 "2023-07-06T13:37:39Z")
Dear Qiime2 members, Previously I am facing some issue with filtering step in dada2 plugin. But now filtering step is ok but I am facing problem in merging. Can any one tell me where is the problem. 0 reads merged in da… --- ## [Low merged percentage after running DADA2](https://forum.qiime2.org/t/low-merged-percentage-after-running-dada2/26789)
**Author:** [@anna2](https://forum.qiime2.org/u/anna2)\ **Replies:** 8\ **Last updated:** [June 20, 2023, 4:21pm UTC](https://forum.qiime2.org/t/low-merged-percentage-after-running-dada2/26789 "2023-06-20T16:21:59Z")
Hello :slight\_smile: I am processing MiSeq libraries (2x300 bp) on V4 16S region (primer pair 515F-806R) with DADA2. However, I am constantly getting a low merged percentage. Based on quality plots I first tried tru… --- ## [Facing merging problem in dada2-plugin](https://forum.qiime2.org/t/facing-merging-problem-in-dada2-plugin/26534)
**Author:** [@Priyanka\_Mishra](https://forum.qiime2.org/u/Priyanka_Mishra)\ **Replies:** 11\ **Last updated:** [June 12, 2023, 1:55pm UTC](https://forum.qiime2.org/t/facing-merging-problem-in-dada2-plugin/26534 "2023-06-12T13:55:28Z")
Initially i am facing problem in filtering where very less reads have passed the filter. But now after setting q20, 50-60% reads passed the filter but I don't know why very less reads have passed on merging. Can anyone … --- ## [What is the acceptable percentage of merged?](https://forum.qiime2.org/t/what-is-the-acceptable-percentage-of-merged/24503)
**Author:** [@tp2c18](https://forum.qiime2.org/u/tp2c18)\ **Replies:** 2\ **Last updated:** [October 21, 2022, 6:05pm UTC](https://forum.qiime2.org/t/what-is-the-acceptable-percentage-of-merged/24503 "2022-10-21T18:05:44Z")
Hello, Could anyone let me know what the acceptable percentage of merged after denoise of paired-end sequences of 16S rRNA (2x300 bp)? I am doing bioinformatics using Qiime2 on 16S rRNA sequences which was sequenced in… --- ## [How to merge q2-sidle output with other results](https://forum.qiime2.org/t/how-to-merge-q2-sidle-output-with-other-results/22823)
**Author:** [@Circle](https://forum.qiime2.org/u/Circle)\ **Replies:** 3\ **Last updated:** [April 21, 2022, 1:04pm UTC](https://forum.qiime2.org/t/how-to-merge-q2-sidle-output-with-other-results/22823 "2022-04-21T13:04:12Z")
Hi, everyone. I'm doing a meta-analysis and one of the studies I included performed 16S 5R sequencing, so I used the plugin q2-sidle to analysis its data, which is amazing and so far I got the results just as I wanted t… --- ## [dada2 paired / with vs without primer / merged huge loss](https://forum.qiime2.org/t/dada2-paired-with-vs-without-primer-merged-huge-loss/21714)
**Author:** [@JeremyTournayre](https://forum.qiime2.org/u/JeremyTournayre)\ **Replies:** 6\ **Last updated:** [January 10, 2022, 7:46am UTC](https://forum.qiime2.org/t/dada2-paired-with-vs-without-primer-merged-huge-loss/21714 "2022-01-10T07:46:33Z")
Hello, I did a dada2 analysis without completely removing my primers on the sequences : the primers have a length of 18 nt for the forward and 21 nt for the reverse. My QIIME2 command: qiime dada2 denoise-paired -… --- ## [DADA2-Low merged output](https://forum.qiime2.org/t/dada2-low-merged-output/21675)
**Author:** [@Joby.robleto](https://forum.qiime2.org/u/Joby.robleto)\ **Replies:** 4\ **Last updated:** [January 10, 2022, 7:31am UTC](https://forum.qiime2.org/t/dada2-low-merged-output/21675 "2022-01-10T07:31:13Z")
Hi everybody! I’m processing MiSeq libraries (2x300bp) on V3-V4 16S region with DADA2. I started importing my data as CasavaOneEightSingleLanePerSampleDirFmt. Then I use cutadapt to remove the primers, then based on the… --- ## [An error was encountered while running qiime feature-table merge](https://forum.qiime2.org/t/an-error-was-encountered-while-running-qiime-feature-table-merge/20420)
**Author:** [@fellora](https://forum.qiime2.org/u/fellora)\ **Replies:** 3\ **Last updated:** [August 9, 2021, 9:51pm UTC](https://forum.qiime2.org/t/an-error-was-encountered-while-running-qiime-feature-table-merge/20420 "2021-08-09T21:51:19Z")
Hi Everyone, I’m working in qiime2-2020.8 and I have this error message. qiime feature-table merge \\ --i-tables boiling\_table.qza --i-tables china\_table.qza --i-tables india\_table.qza --i-tables resto\_table.qza… --- ## [Sequences disappeared after running qiime feature-table merge-seqs](https://forum.qiime2.org/t/sequences-disappeared-after-running-qiime-feature-table-merge-seqs/19965)
**Author:** [@Martin\_Kostovcik](https://forum.qiime2.org/u/Martin_Kostovcik)\ **Replies:** 7\ **Last updated:** [July 27, 2021, 7:23pm UTC](https://forum.qiime2.org/t/sequences-disappeared-after-running-qiime-feature-table-merge-seqs/19965 "2021-07-27T19:23:30Z")
Hi Team, I'm experiencing similar/same issue as mentioned in topic : sequences disappear with this command: qiime feature-table merge-seqs which wasn't resolved. After merging several representative\_sequences.qza artif… --- ## [Losing reads during merging in Dada2](https://forum.qiime2.org/t/losing-reads-during-merging-in-dada2/20221)
**Author:** [@Sam1](https://forum.qiime2.org/u/Sam1)\ **Replies:** 2\ **Last updated:** [July 19, 2021, 11:18am UTC](https://forum.qiime2.org/t/losing-reads-during-merging-in-dada2/20221 "2021-07-19T11:18:43Z")
Dear experts, I have just started working with data from a new sequencing facility and I am losing many more reads during the merging of the pairs in dada2 than I am used to (based on previous experience sampling the sa… --- ## [Rescript merge-taxa non-urgent bug - blank taxon values created when using 'super'](https://forum.qiime2.org/t/rescript-merge-taxa-non-urgent-bug-blank-taxon-values-created-when-using-super/20115)
**Author:** [@smayne11](https://forum.qiime2.org/u/smayne11)\ **Replies:** 2\ **Last updated:** [July 8, 2021, 5:51am UTC](https://forum.qiime2.org/t/rescript-merge-taxa-non-urgent-bug-blank-taxon-values-created-when-using-super/20115 "2021-07-08T05:51:31Z")
I recently ran into an issue when merging taxonomies using the "super" method. The merge completed successfully, but when the merged taxonomy was evaluated using rescript evaluate-taxonomy, the following error was given… --- ## [rescript merge-taxa secondary selection criteria](https://forum.qiime2.org/t/rescript-merge-taxa-secondary-selection-criteria/20102)
**Author:** [@smayne11](https://forum.qiime2.org/u/smayne11)\ **Replies:** 3\ **Last updated:** [July 6, 2021, 6:53am UTC](https://forum.qiime2.org/t/rescript-merge-taxa-secondary-selection-criteria/20102 "2021-07-06T06:53:46Z")
Is there an automatic secondary selection criteria for rescript's merge-taxa method that kicks in when the specified selection criteria is a tie between the two taxonomies? E.g. when merging taxonomies using the "len" m… --- ## [What could do if NCBI-SRA data don't have information about region, primers, barcodes?](https://forum.qiime2.org/t/what-could-do-if-ncbi-sra-data-dont-have-information-about-region-primers-barcodes/19739)
**Author:** [@fellora](https://forum.qiime2.org/u/fellora)\ **Replies:** 1\ **Last updated:** [June 1, 2021, 5:21am UTC](https://forum.qiime2.org/t/what-could-do-if-ncbi-sra-data-dont-have-information-about-region-primers-barcodes/19739 "2021-06-01T05:21:49Z")
Hi Everyone, I’m working in qiime2-2020.8 and I want to analize two raw data from NCBI project (PRJNA279124) hot springs metagenome (ID 279124) - BioProject - NCBI However, this data don't have a paper reference and th… --- ## [Duplicate taxon names after merging biom tables](https://forum.qiime2.org/t/duplicate-taxon-names-after-merging-biom-tables/19447)
**Author:** [@SterlingWright2016](https://forum.qiime2.org/u/SterlingWright2016)\ **Replies:** 3\ **Last updated:** [May 29, 2021, 2:29pm UTC](https://forum.qiime2.org/t/duplicate-taxon-names-after-merging-biom-tables/19447 "2021-05-29T14:29:17Z")
Hi all, I am trying to combine two biom (and qza) tables together. The issue that is coming up is that there are several duplicate taxa rows. For instance, I get two rows with Ruminococcus torques. Does anyone have an i… [Next page](https://forum.qiime2.org/tag/merge/74.md?match_all_tags=true&page=1&tags%5B%5D=merge)