Tag: mothur

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How can I combine different microbiome data sources for further analysis? 0 I have two datasets that are sequenced by Illumina MiSeq contains of V4 region. One is paired ended that sequence length distribution is 250bp, and another is single end reads that sequence length distribution is 150bp. Those datasets…

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Introduction Tea trees (Camellia sinensis (L.) O. Kuntze) are among the most important economic trees in the world, as an important economic crop, which is widely planted in acidic soil in the tropical and sub-tropical zones of China (Liu et al. Citation2019). Meanwhile, tea is an aluminium (Al) accumulating plant that…

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Several studies have indicated the importance of gut microbes in maintaining human health. These microbes are also associated with fundamental physiologic processes, such as aging, drug response, nutrition, and pathophysiologic states (e.g., cardiovascular, metabolic, oncologic, neurological, and autoimmune diseases). To better understand the causal effects between gut microbes and disease…

Phyloseq and Microbiome analyzed in R Data Import and Exploration There are a number of packages advanced in R that make microbiome analysis easy and erzeugt greater figures. At is by times an lot of overlap between this analyse and QIIME – and the choice is yours. Personally I consider…

Back to Bioinformatics Main Menu Mothur GCATemplates available: no Mothur homepage module spider Mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities See syntax for commands when running in command line mode such as in a batch file. mothur.org/wiki/Command_line_mode QIIME GCATemplates available: terra QIIME is an open-source bioinformatics pipeline for…

Hi everyone, Could you please confirm whether the steps outlined in the MIseq SOP of mothur include the removal of adapters and primers sequences from raw reads? If so, could you also specify which command should be used for this purpose? Thank YouRishikesh Our wet lab SOP generates sequences without…

Hi, this is my first post so please tell me if I am not formatting my post correctly! I am trying to open mothur in slurm in interactive mode but it hasn’t been working. Does anyone know how to resolve this? I have looked through this form/googled/played around with various…

mothur Sign Up Log In Log In Popular Make.contigs does not create a count tableCommands in mothur [ERROR]: ‘M03602_424_000000000-KGRP4_1_1108_16589_10118’ is not in your name or count file, please correctmothur bugs Problem cluster.splitCommands in mothur Cluster [ERROR]: expected a number and got OTU.141, quittingmothur bugs How to use Mothur for ITS…

Hi guys, I have a problem with running cluster.split of mothur. I used “cluster.split(fasta=ok.abund.fasta, count=ok.abund.count_table, taxonomy=ok.taxonomy, taxlevel=4, cutoff=0.03, processors=10)” and give this error: Selecting sequences for group Gammaproteobacteria_unclassified (12 of 101)Number of unique sequences: 10484 [WARNING]: ok.abund.count_table does not contain any sequence from the .accnos file.Selected 0 sequences from ok.abund.count_table….

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75010 March 16, 2023, 10:25am 1 make contigs command did not create a count table which need for further analysis. I am using mothur version 1.48. I even try with old versions like 1.43 and 1.43 and did not experience this before.I only got two fasta files and one report…

Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Glöckner, J. et al. Phylogenetic diversity and metagenomics of candidate division OP3. Environ. Microbiol. 12, 1218–1229…

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In my experiment of 16s Data mothur generates an output where we get a taxonomy output file which I need to use for phyloseq r Bioconductor package. I want to visualize my result with this Bioconductor package phyloseq. Still, the problem I am facing is my otu based taxonomy table…

Hello, I ran pcr.seqs() and then align.seqs() and all seemed to be ok. Next, I did screen.seqs, but then I got this error: [ERROR]: ‘M03602_424_000000000-KGRP4_1_1108_16589_10118’ is not in your name or count file, please correct. Does anyone know why this should be happening? Below I am sending the full logfile:mothur…

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As it was shown in Miseq SOP, the most occurring end length of the contig they have fixed the contig length, so in my data what length should I fix in screen.seqs? please do comment. We have sequenced v3-v4 region.Our read length was 301*2 basepair. summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table) Using 20 processors….

query regarding visualization of data in phyloseq package 0 @6d5973d2 Last seen 8 hours ago India I have run mothur pipeline for amplicon sequencing data. I get phyloseq object now I want to visualize various plots like an abundance of taxa, and a comparison of taxa between different samples but…

Dear All, Can anybody explain the problem for make.contigs()? I used mother v.1.48.0. When the oligos option is NOT included in the make.contigs(), the result looks normal and correct. make.file(inputdir=D:\City_bumblebees\z_analysis\microbes\datasets, type=fastq, prefix=framgement)make.contigs(file=framgement.files)summary.seqs(fasta=framgement.trim.contigs.fasta, count=framgement.contigs.count_table) The groups have the Group_0, with a total of 1259009 sequences (see below) Group count:Group_0 62092Group_1 65104Group_10…

DYH March 1, 2023, 2:37am 1 After completing make.contigs, I ran sub.sample, but the following error occurred: mothur > sub.sample(fasta=stability.trim.contigs.fasta,count=stability.contigs.count_table,persample=T,size=10000)[ERROR]: your fasta file contains 239780 sequences, and your count file contains 147069 unique sequences, please correct. I am running the script on linux, but this problem does not occur on…

DYH March 2, 2023, 1:43pm 1 Specific problem ： It shows that I spliced 354959 sequences in total， but the summary.seqs of fasta file shows 570747 sequences. I do not know why this situation occues Group count: Group_0 46079 Group_1 40237 Group_2 44860 Group_3 72493 Group_4 48151 Group_5 103139 Total…

Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193–199 (2009). Article  CAS  PubMed  Google Scholar  Graham, E. B. et al. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front. Microbiol. 7, 214 (2016). Article  PubMed  PubMed Central  Google Scholar …

Site sampling Main field recognition and sampling of the Red Stone outcrop took place on August, 2019, although subsequent site sampling also took place in February, May, August and October of 2021. After surveying the surroundings, the most continuous exposure was selected to take advantage of the best section traverse…

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Is there an update for the following SOP: 16S Microbial Analysis with mothur (extended) 1 We keep getting an error after the unique.seq command. Help!! Help! SOP update? Error after Unique.seq Help! SOP update? Error after Unique.seq Mhayes 6d Is there an update for the following SOP: 16S Microbial Analysis…

Is there an update for the following SOP: 16S Microbial Analysis with mothur (extended) 1 We keep getting an error after the unique.seq command. Help!! Help! SOP update? Error after Unique.seq Help! SOP update? Error after Unique.seq Mhayes 6d Is there an update for the following SOP: 16S Microbial Analysis…

Hi- I have performed alignment without any prior screening. After alignment (withalign.seqs) I am getting such sequence distribution: Using 16 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 11550 231 0 3 1 2.5%-tile: 1968 11550 252 0 3 261901 25%-tile: 1968 11552 253 0 4 2619004 Median: 1968…

Sam92 January 25, 2023, 6:37am #1 Hi I am running in to a problem with the pre.cluster step. I am running it as a batch file and the output in mothur log file is as follows. mothur > summary.seqs(fasta=current) Using MethodF2.trim.pcr.trim.good.unique.good.filter.unique.fasta as input file for the fasta parameter. Using 40…

Dear mothur enthusiasts, A colleague advised me to try and run picrust on my dataset in order to get some functional inference from 16S sequences. He told me to “classify the OTU on GreenGenes” and prepare a biom file. I have tried to follow the commands listed in an earlier…

Hira October 30, 2022, 8:20am #1 After making contigs, here is the summary of my data. And the summary of contigs report: mothur > screen.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table, maxambig=0, maxlength=275, maxhomop=8) It took 28 secs to screen 1896836 sequences, removed 1896836. /******************************************/Running command: remove.seqs(accnos=/users/hiraabid/desktop/mothur/Paddy_Fish_NGS_RawData/stability.trim.contigs.bad.accnos.temp, count=/users/hiraabid/desktop/mothur/Paddy_Fish_NGS_RawData/stability.contigs.count_table)Removed 1896836 sequences from /users/hiraabid/desktop/mothur/Paddy_Fish_NGS_RawData/stability.contigs.count_table.[WARNING]: /users/hiraabid/desktop/mothur/Paddy_Fish_NGS_RawData/stability.contigs.count_table contains only…

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I have a data set of 2×150 reads of 54 pairs of 16S v4 metagenomic sequences from NCBI sra of gastritis patients. When I previously ran the sequences through mothur, the screen.seqs after silva alignment removed sufficient number of sequences. mothur > screen.seqs(fasta=current, count=current, start=2, end=13426)Using Ulcer_Donors\stability.trim.contigs.count_table as input file…

Hello, I ran into this problem while running mothur on a server. mothur > merge.files(input=saraCPERF.trim.contigs.unique.good.good.filter.unique .precluster.denovo.vsearch.pick.fasta-combinedphyto.good.filter.unique.precluste r.denovo.vsearch.fasta, output=combined_saraCPERF.fasta) Unable to open combinedphyto.good.filter.unique.precluster.denovo.vsearch.fasta. Trying mothur’s executable directory combinedphyto.good.filter.unique.precluste r.denovo.vsearch.fasta. Unable to open combinedphyto.good.filter.unique.precluster.denovo.vsearch.fasta. Unable to open ▒!q▒cod.filter.unique.precluster.denovo.vsearch.fasta. Trying mot hur’s executable directory ‘qod.filter.unique.precluster.denovo.vsearch.fasta. Unable to open ‘qod.filter.unique.precluster.denovo.vsearch.fasta. free(): double free detected…

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Sam92 April 5, 2022, 3:07am #1 Hello, I want to bin my sequences in to phylotypes according to their classification. I used the following command, phylotype(taxonomy=year1.trim.pcr.trim.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.0.03.cons.taxonomy) After running this, it crashed mothur instantly. I also tried running it on servers and got the same results.I am using mothur v.1.45.2 Please…

Hi all, I am using the mothur toolsuite on Galaxy to attempt to process duodenal microbiome samples in humans. The datasets I am using are paired reads generated by WGS. I am directly following this guide: training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html I’m stuck on the OTU Clustering section for my data samples, specifically the…

Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared…

16SMaRT is a bioinformatics analysis pipeline for 16s rRNA gene sequencing data. 16SMaRT is a “one-click” solution towards performing microbial community analysis of amplicon sequencing data. 16SMaRT aims to be your go-to solution for your next microbiome/metagenomics project. The primary objective of 16SMaRT analysis is to determine what genes are…

Introduction Atopic dermatitis (AD) is the most common chronic, and recurrent inflammatory skin disease. The prevalence of AD varies throughout the world and still increasing. In developing countries, 10–20% of children and 1–3% of adults are affected by AD. This disease is characterized by significant itching.1,2 Intense itching causes trauma…

Clustering in virome 0 Please, can someone suggest to me a bioinformatics tool for de-novo clustering in virome? I would like to use DADA2 (as AVS clustering tool) plugin of QIIME2, but it looks specific for 16S rRNA gene amplicon sequencing and I am not sure it will work well…

Hi Andreas, Andreas Tille, on 2021-10-21: > In file included from addtargets2.cpp:3: > myutils.h:176:1: error: reference to ‘byte’ is ambiguous Since C++ 2017, the std::byte type is defined: > 176 | byte *ReadAllStdioFile(FILE *f, off_t &FileSize); > | ^~~~ > In file included from /usr/include/c++/11/bits/stl_algobase.h:61, > from /usr/include/c++/11/bits/char_traits.h:39, > from…

Introduction Diabetic nephropathy (DN) is characterized by kidney function loss caused by diabetes mellitus.1 Almost one-third of patients with diabetes have DN, and the prevalence of DN is increasing worldwide.2 DN is one of the most important factors of chronic kidney disease and end-stage renal disease (ESRD). The signs and…

Which of the following statements are true about the commands used… in mothur during the process of generating contigs, filtering and merging the contigs and counting contigs?Question 17 options: The make.contigs command will extract the sequence and quality score data from your fastq files, create the reverse complement of the…

phyloseq Handling and analysis of high-throughput microbiome census data. Detecting the periodontal pathogens at the subgingival plaque requires skilled professionals to collect samples. Import mothur list and group files and return an otu_table. In a randomized, double-blind, placebo-controlled trial, we assessed the effect of Lactobacillus reuteri supplementation, from birth to…

Dear Galaxy maintainers, I would like to ask for an update of the Mothur version on the usegalaxy server.Currently the installed version is 1.39.5.0, whereas the latest version is 1.46.1 (on mothur.org). The more recent version allows for converting DADA2 count table output to shared data format using the command…

Ask questionsAdd ASV/OTU to taxonomy string for sequences forum.mothur.org/t/otu-and-asv-in-taxonomy-file/20988 mothur/mothur Answer questions Preliminary output example: ASV_OTULabel ASV_Abundance Taxonomy_Clustered_OTULabel Otu0001 12196 Bacteria;”Bacteroidetes”;”Bacteroidia”;”Bacteroidales”;”Porphyromonadaceae”;”Porphyromonadaceae”_unclassified;Otu001; Otu0002 8829 Bacteria;”Bacteroidetes”;”Bacteroidia”;”Bacteroidales”;”Porphyromonadaceae”;”Porphyromonadaceae”_unclassified;Otu002; … Otu0331 4 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospiraceae_unclassified;Otu041; Otu0332 4 Bacteria;”Bacteroidetes”;”Bacteroidia”;”Bacteroidales”;”Porphyromonadaceae”;”Porphyromonadaceae”_unclassified;Otu005; Otu0333 4 Bacteria;”Proteobacteria”;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Acinetobacter;Otu259; Otu0334 4 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospiraceae_unclassified;Otu187; … Otu2423 1 Bacteria;”Bacteroidetes”;”Bacteroidia”;”Bacteroidales”;”Porphyromonadaceae”;”Porphyromonadaceae”_unclassified;Otu012; Otu2424 1 Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Oscillibacter;Otu175; useful! Read more here: Source link