Tag: QIIME2

autopkgtest needs update for new version of python-decorator)

Hi, I’d like to point out to this serious bug. Steffen, would you mind koordinating (not doing alone) an upgrade of the qiime infrastructure to make sure everything will go smoothly? Kind regards Andreas. Am Thu, Jun 30, 2022 at 11:30:21AM +0200 schrieb Paul Gevers: > Source: qiime > Version:…

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can i skip cutadapt?? – User Support

recently i receive rowdata from NGS center..and i start analysis using QIIME2 i want ‘cutadapt’, so i ask primer sequence to NGS center..but center reply to me “it is secret” if it is neccessery, i request to NGS center…. thank u for reading Hi @svbreqwaiu01, You do not need to…

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How to normalize biom table from qiime2 to edgeR on Rstudio?

How to normalize biom table from qiime2 to edgeR on Rstudio? 0 Hi, I’m new in this of bioinformatics, I’m making a metagenome analysis of ITS region, then, I want to normalize my data, so i exported a biom table from qiime2 with taxonomic annotations, and then I converted that…

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losing large amount of reads when using Qiime2 vsearch joinpairs command

losing large amount of reads when using Qiime2 vsearch joinpairs command 0 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…

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installation of qiime2 on pycharm with anaconda interperter

I’m a relatively new qiime2 (bioinformatics tool based on python language) and python user. So far, I have been using qiime2 inside a virtual machine, which is ok but not great. Since I’m taking a python course and have gotten used to work with pycharm, I’m trying to install the…

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Qiime2 Exclude Seqs with FASTQ as query data.

Qiime2 Exclude Seqs with FASTQ as query data. 0 Hello, I am working with FASTQ files and I want to filter them based on the alignment with references sequences in FASTA format. I decided to use QIIME2 for this. So I imported both FASTA and FASTQ files to the required…

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QIIME2 for metagenomics analysis – githubhot

Name of the tool QIIME2 Tool homepage qiime2.org/ Tool description QIIME2 supports the microbiome data visualization with different types of analysis (e.g. ANCOM, alpha diversity, beta diversity, etc.) Tool output ANCOM_example_output.zip Attached files are some example ANCOM output from QIIME2. Their format is tsv files with the column name information…

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r – RC Bray function not accepting phyloseq otu_table as argument

I am using James Stegen et al’s code here to calculate an abundance-weighted raup-crick value for my 16S dataset. I load in my phyloseq object then extract the otu_table. I then use the otu_table as the spXsite argument in the function raup_crick_abundance(). My otu_table is available as a dput() below…

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A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2

%PDF-1.5 % 211 0 obj > endobj 295 0 obj >stream application/pdf Snaq: A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2 2022-03-11T02:09:25Z LaTeX with hyperref 2022-03-13T05:02:28-07:00 2022-03-13T05:02:28-07:00 pdfTeX-1.40.23 False This is pdfTeX, Version 3.141592653-2.6-1.40.23 (TeX Live 2021) kpathsea version 6.3.3 uuid:4f5ae20a-1dd2-11b2-0a00-300927edca00 uuid:4f5ae20e-1dd2-11b2-0a00-380000000000 endstream endobj 212 0 obj > endobj…

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Picrust2 not recognized – Community Plugin Support

Ok. So I’m doing this in a computing cluster for reference, and before doing anything I can see these conda environments: (base) [cjone228@jhu.edu@bc-login01 ~]$ conda env list # conda environments: # base * /home-1/cjone228@jhu.edu/miniconda3 picrust2 /home-1/cjone228@jhu.edu/miniconda3/envs/picrust2 qiime2-2019.10 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2019.10 qiime2-2019.7 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2019.7 qiime2-2020.2 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2020.2 qiime2-2020.6 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2020.6 Now when I try and install…

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How to order sample names with the phyloseq object for heatmap

Hello!I am new to the Rstudio!I can’t find a tutorial, or instructions for ordering our samples in the heatmapI have created the phyloseq object with the next scripts physeq<-qza_to_phyloseq(features=”file path/rarefied_table.qza”,metadata=”file path/Metadata.tsv”)taxonomy = read.csv(“file path/taxonomy.csv”,sep=”,”,row.names=1)taxonomy =as.matrix(taxonomy)TAX = tax_table(taxonomy)data_full<-merge_phyloseq(physeq,TAX) then I use ph = tax_glom(data_full, taxrank=’Genus’,NArm=FALSE)TOP = names(sort(taxa_sums(ph), TRUE)[1:20])TOPp = prune_taxa(TOP, ph)plot_heatmap(TOPp,…

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Error rates could not be estimated — unsure why – Technical Support

I’m running dada2 on paired end data and getting the same error over and over again. My data are from an 150 PE run on an Illumina iSeq machine, sequencing a 16s fragment for vertebrates. The samples were demultiplexed by Casava based on the i5 and i7 adapters. Some samples…

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Quality-filter “‘NoneType’ object is not subscriptable” – Technical Support

Hello, I’m trying to use q2 quality-filter on the Mockrobiota ‘Extreme’ data (mock-12) before denoising with deblur, using the command qiime quality-filter q-score –i-demux demuxed_sequences.qza –o-filtered-sequences quality_filtered_seqs.qza –o-filter-stats quality_filtered_stats.qza –verbose However, I get the following error when I try to run it on my data: Traceback (most recent call last):File…

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qiime2/q2cli – githubmate

A click-based command line interface for QIIME 2. Installation and getting help Visit qiime2.org to learn more about q2cli and the QIIME 2 project. Enabling tab completion Bash To enable tab completion in Bash, run the following command or add it to your .bashrc/.bash_profile: ZSH To enable tab completion in…

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An error about using DADA2 in QIIME2 – Community Plugin Support

Hi everyone,I analyzed my pacbio data according to this PR, but an error was happened: Error in h(simpleError(msg, call)) : Error: invalid class “SRFilterResult” object: superclass “Mnumeric” no t defined in the environment of the object’s class stop Traceback (most recent call last): File “/home/xxx/miniconda3/envs/qiime2-2021.4/lib/python3.8/site- packages/q2_dada2/_denoise.py”, line 361, in denoise_ccs…

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Bioenv diversity error with qiime version 2021.4, but not with 2020.2 – Technical Support

203967.metadata.tsv (702 Bytes) table-trim55126.qza (58.4 KB) rooted-tree.qza (76.7 KB) I have qiime 2020.2 and qiime 2021.4 installed via conda. Using the attached files, I ran the following command which succeeded in both qiime version 2020.2 and version 2021.4: qiime diversity core-metrics-phylogenetic –verbose –i-phylogeny rooted-tree.qza –i-table table-trim55126.qza –m-metadata-file 203967.metadata.tsv –p-sampling-depth 300…

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How to differenciate between 16s hypervariables regions using QIIME2 ? – User Support

M_F: May i search the sequences on ncbi for example correponding to v4 domain No, NCBI probably would not have such sequences in an easily indexed form but I could be wrong. Rather, grab some reference sequences (can be a random subsample, do not need all of them) and use…

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Import problem: Not a(n) QIIME1DemuxFormat file – Technical Support

Hi @emiliomastriani, Did you download the sequences form sra?This previous question may give you some help: Hi there, I am familiar with QIIME1 but relatively new with QIIME2. I have gotten my raw file in the past from a facility in the CASAVA pair ended demultiplexed format and I had…

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qiime2-import data from non-working directory – User Support

Hello, qiime2 users community! I have the following set-up: a huge collection of .fastq files which I would like to process with the dada2 pipeline a remote cluster of servers with the separated storage where those files are stored, and the working machines for computing. Question: Is it possible to…

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q2-krona: Plugin for creating Krona plots – Plugins

Hello everyone, I’ve finally got time from work and finished the plugin. Special thanks to @Nicholas_Bokulich for suggesting making my own plugin, and @thermokarst for revision. The plugin is available at my github page (see: github.com/kaanb93/q2-krona). Simply, Krona is a tool to create interactive multi-layered pie charts. Here is an…

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Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

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Still Not Use QIIME2 for Amplicon Analysis? You’re OUT!

I want to share with you a powerful tool named QIIME 2. It’s handy for Amplicon analysis. What is QIIME 2? The Quantitative Insights Into Microbial Ecology (QIIME) microbiome bioinformatics platform has supported many microbiome studies and gained a broad user and developer community. QIIME 2™(qiime2.org) is a new version…

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how to demultiplex paired end reads when R1 and R2 are identified by two different substrings?

I am struggling with finding a solution to a problem which seems easy but it’s not. I found many many questions that seems to be related (and I believe they are) but they are confusing and you never know which one fits your case. So there we go. I’ll try…

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