# \#paired-end **URL:** https://forum.qiime2.org/tag/paired-end/90.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Which position is best for trimming in a paired-end approach?](https://forum.qiime2.org/t/which-position-is-best-for-trimming-in-a-paired-end-approach/32341)
**Author:** [@joaomiranda](https://forum.qiime2.org/u/joaomiranda)\ **Replies:** 10\ **Last updated:** [January 24, 2025, 10:00pm UTC](https://forum.qiime2.org/t/which-position-is-best-for-trimming-in-a-paired-end-approach/32341 "2025-01-24T22:00:11Z")
Hello qiime community! I'm bringing some questions about the pre-denoising step, the scan on the quality of my sequences and the best chioice about where to trim my reads. First: I'm using the qiime2-amplicon-2024.10 a… --- ## [How to import paried end sequencing files and full length sequencing files together into qiime2?](https://forum.qiime2.org/t/how-to-import-paried-end-sequencing-files-and-full-length-sequencing-files-together-into-qiime2/31939)
**Author:** [@Yuhang\_Wu](https://forum.qiime2.org/u/Yuhang_Wu)\ **Replies:** 4\ **Last updated:** [November 25, 2024, 6:28am UTC](https://forum.qiime2.org/t/how-to-import-paried-end-sequencing-files-and-full-length-sequencing-files-together-into-qiime2/31939 "2024-11-25T06:28:29Z")
Hi every one, I have learn the qiime2 amplicon pipeline for paired-end sequencing files and these official tutorials are really helpful. There are some paired end sequencing files and full length amplicon files in my re… --- ## [Error importing manifest file; paired end, demultiplexed data](https://forum.qiime2.org/t/error-importing-manifest-file-paired-end-demultiplexed-data/31339)
**Author:** [@tannerbahm](https://forum.qiime2.org/u/tannerbahm)\ **Replies:** 3\ **Last updated:** [September 5, 2024, 5:56pm UTC](https://forum.qiime2.org/t/error-importing-manifest-file-paired-end-demultiplexed-data/31339 "2024-09-05T17:56:30Z")
Hi! I'm trying to import demultiplexed, paired end sequences via a manifest file. This is the code I have been running: qiime tools import --type 'SampleData\[PairedEndSequencesWithQuality\]' --input-path /Users/tannerba… --- ## [Error running qiime denoise-paired (return code 1: Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.))](https://forum.qiime2.org/t/error-running-qiime-denoise-paired-return-code-1-error-in-geterrors-err-enforce-true-error-matrix-is-null/31241)
**Author:** [@camrynbigelow](https://forum.qiime2.org/u/camrynbigelow)\ **Replies:** 3\ **Last updated:** [August 27, 2024, 8:07pm UTC](https://forum.qiime2.org/t/error-running-qiime-denoise-paired-return-code-1-error-in-geterrors-err-enforce-true-error-matrix-is-null/31241 "2024-08-27T20:07:55Z")
Hello! I am running qiime2 2024.5 on a PC with paired-end demultiplexed sequences. I keep getting code 1 errors when running the following code. I tried decreasing my threads (from 0 to 15 to 8 to 4) as suggested in a p… --- ## [Error qiime tools import](https://forum.qiime2.org/t/error-qiime-tools-import/31171)
**Author:** [@Vicky\_Rodriguez](https://forum.qiime2.org/u/Vicky_Rodriguez)\ **Replies:** 1\ **Last updated:** [August 17, 2024, 7:48pm UTC](https://forum.qiime2.org/t/error-qiime-tools-import/31171 "2024-08-17T19:48:44Z")
Hello I have a problem, was running the first lines of code, the file. qza is created but throws these error lines (Imagenes 1 and 2). Then I tried to visualize the . qzv but it tells me that the file. qza is not an arti… --- ## [Importing files in Casava format - md5sum not found](https://forum.qiime2.org/t/importing-files-in-casava-format-md5sum-not-found/30826)
**Author:** [@Ashoi\_Dantra](https://forum.qiime2.org/u/Ashoi_Dantra)\ **Replies:** 2\ **Last updated:** [August 7, 2024, 6:38am UTC](https://forum.qiime2.org/t/importing-files-in-casava-format-md5sum-not-found/30826 "2024-08-07T06:38:11Z")
Hi, student here. I have used CASAVA format before and have never faced this issue. I just used the code qiime tools import --type 'SampleData\[PairedEndSequencesWithQuality\]' --input-path /export/home/a-e/adantra/i… --- ## [How to import paired end data from miseq?](https://forum.qiime2.org/t/how-to-import-paired-end-data-from-miseq/30130)
**Author:** [@ehdud0505](https://forum.qiime2.org/u/ehdud0505)\ **Replies:** 2\ **Last updated:** [May 8, 2024, 4:54am UTC](https://forum.qiime2.org/t/how-to-import-paired-end-data-from-miseq/30130 "2024-05-08T04:54:33Z")
Hello, everyone. I'm struggling with data importing right now. I'm using qiime2.2024.2 version. The data is obtained via miseq and the files are in the form of OO-forward.fastq.qz, OO-reverse.fastq.qz. Barcode is expe… --- ## [Paired end: 2x151 vs 2x250 for V4](https://forum.qiime2.org/t/paired-end-2x151-vs-2x250-for-v4/17382)
**Author:** [@Mike\_McFarlin](https://forum.qiime2.org/u/Mike_McFarlin)\ **Replies:** 7\ **Last updated:** [June 26, 2023, 2:11pm UTC](https://forum.qiime2.org/t/paired-end-2x151-vs-2x250-for-v4/17382 "2023-06-26T14:11:50Z")
Hi everyone, I am about to send samples of extracted DNA out to a lab for library preparation and sequencing. I will be using the 515f-806r primers for the V4 region. I am unsure whether I should use 2x151 or 2x250 pair… --- ## [Importing data / using old and new FASTQ files to compare](https://forum.qiime2.org/t/importing-data-using-old-and-new-fastq-files-to-compare/26326)
**Author:** [@zahra](https://forum.qiime2.org/u/zahra)\ **Replies:** 2\ **Last updated:** [May 5, 2023, 5:47pm UTC](https://forum.qiime2.org/t/importing-data-using-old-and-new-fastq-files-to-compare/26326 "2023-05-05T17:47:17Z")
Good afternoon! I am attempting to compare 16S rRNA microbiome data from an experiment I have performed recently to a published study from 2013. I've downloaded the samples and converted them from SRA to FASTQ from NCBI… --- ## [More sequences were provided than barcodes](https://forum.qiime2.org/t/more-sequences-were-provided-than-barcodes/25206)
**Author:** [@flira](https://forum.qiime2.org/u/flira)\ **Replies:** 5\ **Last updated:** [January 12, 2023, 8:43pm UTC](https://forum.qiime2.org/t/more-sequences-were-provided-than-barcodes/25206 "2023-01-12T20:43:01Z")
Hi All, I am looking for some insightful answers to solve this problem: Plugin error from demux: More sequences were provided than barcodes. If someone can help me, I appreciate it. FL --- ## [issue with demultiplexing paired end reads](https://forum.qiime2.org/t/issue-with-demultiplexing-paired-end-reads/24216)
**Author:** [@LauraMason](https://forum.qiime2.org/u/LauraMason)\ **Replies:** 4\ **Last updated:** [September 27, 2022, 2:33pm UTC](https://forum.qiime2.org/t/issue-with-demultiplexing-paired-end-reads/24216 "2022-09-27T14:33:30Z")
Hello @Afaf and I are having an issue with demultiplexing (or possibly denoising) end reads as well. We used demux cut-adapt in qiime2-2022.8, and we are looking for some guidance Briefly, we received multiplexed forwa… --- ## [Demux sequence summary length much smaller than actual sequences are/should be](https://forum.qiime2.org/t/demux-sequence-summary-length-much-smaller-than-actual-sequences-are-should-be/23812)
**Author:** [@elerin](https://forum.qiime2.org/u/elerin)\ **Replies:** 4\ **Last updated:** [August 30, 2022, 1:53am UTC](https://forum.qiime2.org/t/demux-sequence-summary-length-much-smaller-than-actual-sequences-are-should-be/23812 "2022-08-30T01:53:21Z")
Hi all! My problem is similar to this topic, however I have follow up questions I can't post in that topic: Demultiplexed sequence length summary identical forward and reverse for emp paired end reads - User Support - … --- ## [losing large amount of reads when using vsearch joinpairs](https://forum.qiime2.org/t/losing-large-amount-of-reads-when-using-vsearch-joinpairs/23038)
**Author:** [@Johanna\_Lisa\_Bosch](https://forum.qiime2.org/u/Johanna_Lisa_Bosch)\ **Replies:** 3\ **Last updated:** [May 17, 2022, 7:20am UTC](https://forum.qiime2.org/t/losing-large-amount-of-reads-when-using-vsearch-joinpairs/23038 "2022-05-17T07:20:35Z")
Hi there! I am running various sediment samples (Illumina for amplicon 16S - V4V5 sequencing) through the Qiime2 pipeline, however when I use vsearch joinpairs to join my paired end reads I lose a bunch of reads. For ref… --- ## [Benchmarking alternative methods of read-joining in QIIME 2](https://forum.qiime2.org/t/benchmarking-alternative-methods-of-read-joining-in-qiime-2/21939)
**Author:** [@amirza](https://forum.qiime2.org/u/amirza)\ **Replies:** 3\ **Last updated:** [January 24, 2022, 6:25pm UTC](https://forum.qiime2.org/t/benchmarking-alternative-methods-of-read-joining-in-qiime-2/21939 "2022-01-24T18:25:08Z")
Has any benchmarking been done for the tutorial on Alternative methods of read-joining in QIIME 2? I would like to know if joining paired-end reads that have lots of overlap (e.g. F and R 150 bp reads sequenced from V4 r… --- ## [Problem importing SAMPLE is not a(n) FastqGzFormat file: Missing sequence for record beginning on line 33313](https://forum.qiime2.org/t/problem-importing-sample-is-not-a-n-fastqgzformat-file-missing-sequence-for-record-beginning-on-line-33313/21745)
**Author:** [@NickoleV](https://forum.qiime2.org/u/NickoleV)\ **Replies:** 1\ **Last updated:** [December 28, 2021, 8:18pm UTC](https://forum.qiime2.org/t/problem-importing-sample-is-not-a-n-fastqgzformat-file-missing-sequence-for-record-beginning-on-line-33313/21745 "2021-12-28T20:18:59Z")
Hi all! I am using QIIME2 version 2021.2. I amtrying to import some 16S paired end data using the following command: qiime tools import --type 'SampleData\[PairedEndSequencesWithQuality\]' --input-path Seqs --input-form… --- ## [Problems with demultiplexing dual-indexed pair-end sequences from MiSeq, Illumina](https://forum.qiime2.org/t/problems-with-demultiplexing-dual-indexed-pair-end-sequences-from-miseq-illumina/21571)
**Author:** [@Viktoria](https://forum.qiime2.org/u/Viktoria)\ **Replies:** 4\ **Last updated:** [December 13, 2021, 6:02pm UTC](https://forum.qiime2.org/t/problems-with-demultiplexing-dual-indexed-pair-end-sequences-from-miseq-illumina/21571 "2021-12-13T18:02:09Z")
Hello! I have multiplexed data from MiSeq, Illumina - 2 fastq.gz files (forward and reverse reads). All my samples are dual-indexed (the same forward barcode but different reverse barcodes) so I create 2 metadata files (… --- ## [Error with dada2 (return code 1) isBimeraDenovoTable](https://forum.qiime2.org/t/error-with-dada2-return-code-1-isbimeradenovotable/21308)
**Author:** [@mikatsume](https://forum.qiime2.org/u/mikatsume)\ **Replies:** 7\ **Last updated:** [November 17, 2021, 5:44pm UTC](https://forum.qiime2.org/t/error-with-dada2-return-code-1-isbimeradenovotable/21308 "2021-11-17T17:44:54Z")
Hi, this is my first time using qiime, the thing is the sequences that were given to me were paired-end fastq files (demultiplexed) so i followed the casava import tutorial. then i tried to run dada2 to denoise: qiim… --- ## [Need to trim primers but this will prevent merging sequences?](https://forum.qiime2.org/t/need-to-trim-primers-but-this-will-prevent-merging-sequences/20944)
**Author:** [@MicrobeManager](https://forum.qiime2.org/u/MicrobeManager)\ **Replies:** 11\ **Last updated:** [October 4, 2021, 7:19pm UTC](https://forum.qiime2.org/t/need-to-trim-primers-but-this-will-prevent-merging-sequences/20944 "2021-10-04T19:19:01Z")
I have a 16s dataset consisting of demultiplexed Illumina paired-end reads, each at 250 bp using primers 341F CCTACGGGNGGCWGCAG (17nt) and 805R GACTACHVGGGTATCTAATCC (21nt). I successfully imported the data manifest and … --- ## [Importing Data on QIIME2 -barcode file not recognized](https://forum.qiime2.org/t/importing-data-on-qiime2-barcode-file-not-recognized/20558)
**Author:** [@Ksalg](https://forum.qiime2.org/u/Ksalg)\ **Replies:** 2\ **Last updated:** [August 26, 2021, 11:30pm UTC](https://forum.qiime2.org/t/importing-data-on-qiime2-barcode-file-not-recognized/20558 "2021-08-26T23:30:10Z")
Hello, Super new to QIIME2 and would appreciate suggestions on my current issue. I'm trying to import my data and convert the files into qza format. However, when I run the code I receive an error stating that the barco… --- ## [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… --- ## [Lose many reads after running cut-adapt and join-pairs](https://forum.qiime2.org/t/lose-many-reads-after-running-cut-adapt-and-join-pairs/19276)
**Author:** [@sjcochran](https://forum.qiime2.org/u/sjcochran)\ **Replies:** 5\ **Last updated:** [April 19, 2021, 4:34pm UTC](https://forum.qiime2.org/t/lose-many-reads-after-running-cut-adapt-and-join-pairs/19276 "2021-04-19T16:34:56Z")
Hello everyone! I am new to the QIIME2 forum and am hoping to get some assistance with a preliminary dataset. I have demultiplexed paired reads from the fungal ITS1 region and I am using QIIME2 on a VirtualBox. I import… --- ## [dada2 maxMismatch](https://forum.qiime2.org/t/dada2-maxmismatch/18757)
**Author:** [@alison](https://forum.qiime2.org/u/alison)\ **Replies:** 1\ **Last updated:** [March 5, 2021, 7:47pm UTC](https://forum.qiime2.org/t/dada2-maxmismatch/18757 "2021-03-05T19:47:17Z")
Is there a way to use the maxMismatch flag in dada2 when running in qiime2? I noticed the default is zero mismatches, and I suspect that is why so much of my data is being lost in merging (in Qiime1 I used to set this a… --- ## [different histograms despite same analysis for two different batches](https://forum.qiime2.org/t/different-histograms-despite-same-analysis-for-two-different-batches/18308)
**Author:** [@tinabui04](https://forum.qiime2.org/u/tinabui04)\ **Replies:** 1\ **Last updated:** [January 31, 2021, 10:39am UTC](https://forum.qiime2.org/t/different-histograms-despite-same-analysis-for-two-different-batches/18308 "2021-01-31T10:39:48Z")
I created a sequence manifest and am demultiplexing. There are two batches of sequences (batch A and B). I'm doing quality control on them separately and then merging them later. However, after demultiplexing each batch,… --- ## [Export merged paired-end fastq files](https://forum.qiime2.org/t/export-merged-paired-end-fastq-files/18052)
**Author:** [@kms285](https://forum.qiime2.org/u/kms285)\ **Replies:** 2\ **Last updated:** [January 14, 2021, 7:41pm UTC](https://forum.qiime2.org/t/export-merged-paired-end-fastq-files/18052 "2021-01-14T19:41:53Z")
I need to merge demultiplexed paired-end reads to a single fastq file for each sample for uploading to a repository. Is there a way to obtain these files from QIIME2, rather than using a completely separate tool like FLA… --- ## [can we convert paired-end-demux.qza to fastq files](https://forum.qiime2.org/t/can-we-convert-paired-end-demux-qza-to-fastq-files/17590)
**Author:** [@drmusk](https://forum.qiime2.org/u/drmusk)\ **Replies:** 3\ **Last updated:** [November 26, 2020, 8:21pm UTC](https://forum.qiime2.org/t/can-we-convert-paired-end-demux-qza-to-fastq-files/17590 "2020-11-26T20:21:00Z")
Hello Colleagues I made paired-end-demux.qza using a manifest file and paired-end reads. I lost or deleted fastq files. Now I need them for some good reason. Is it possible to convert paired-end-demux.qza to fastq files… --- ## [cutadapt demux-paired demuxes some but not all samples](https://forum.qiime2.org/t/cutadapt-demux-paired-demuxes-some-but-not-all-samples/17132)
**Author:** [@mchimenti](https://forum.qiime2.org/u/mchimenti)\ **Replies:** 1\ **Last updated:** [October 19, 2020, 8:01pm UTC](https://forum.qiime2.org/t/cutadapt-demux-paired-demuxes-some-but-not-all-samples/17132 "2020-10-19T20:01:11Z")
Hello: I am attempting to demultiplex paired-end, 300 bp reads from a MiSeq run with dual-indexed data. Barcodes are in the reads. I checked with 'grep' and they are the first 8 nt in both R1 and R2 reads. They are n… --- ## [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… --- ## [Diversity changes within an environmental sample at different conditions](https://forum.qiime2.org/t/diversity-changes-within-an-environmental-sample-at-different-conditions/16972)
**Author:** [@sakshi](https://forum.qiime2.org/u/sakshi)\ **Replies:** 2\ **Last updated:** [October 12, 2020, 11:28am UTC](https://forum.qiime2.org/t/diversity-changes-within-an-environmental-sample-at-different-conditions/16972 "2020-10-12T11:28:39Z")
Hello all, I am new user and have no background of bioinformatics or microbiome analysis so the questions might be very basic. I have Illumina 16s paired end sequences for an environmental sample V3-V4. I want to study… --- ## [Handling paired-end dual indexed Illumina FASTQ files](https://forum.qiime2.org/t/handling-paired-end-dual-indexed-illumina-fastq-files/16175)
**Author:** [@Lou](https://forum.qiime2.org/u/Lou)\ **Replies:** 3\ **Last updated:** [August 20, 2020, 7:45pm UTC](https://forum.qiime2.org/t/handling-paired-end-dual-indexed-illumina-fastq-files/16175 "2020-08-20T19:45:59Z")
Dear QIIME2-community, I am totally new to QIIME and QIIME2. I want to analyse paired-end dual indexed Illumina reads, which means I have 4 FASTQ files (R1 and R2 with microbial sequences, I1 and I2 with barcode sequenc… --- ## [Error when running dada2 denoise-paired (return code 1)](https://forum.qiime2.org/t/error-when-running-dada2-denoise-paired-return-code-1/15222)
**Author:** [@lineroager](https://forum.qiime2.org/u/lineroager)\ **Replies:** 3\ **Last updated:** [June 4, 2020, 4:41pm UTC](https://forum.qiime2.org/t/error-when-running-dada2-denoise-paired-return-code-1/15222 "2020-06-04T16:41:54Z")
Hello there! I am running qiime2 2020.2 on a MacBook through a remote ssh server, installed with miniconda. I am working with some paired-end demultiplexed sequences (non-Casava), which I have successfully imported with… [Next page](https://forum.qiime2.org/tag/paired-end/90.md?match_all_tags=true&page=1&tags%5B%5D=paired-end)