Tag: mothur

Screen.seqs result varying – Commands in mothur

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…

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Merge.file do not like CAP letters – mothur bugs

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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Bioinformatics Software Market Outlook: Post Covid-19 Scenario by 2029

California (United States) – The Bioinformatics Software Market Research Report is a professional asset that provides dynamic and statistical insights into regional and global markets. It includes a comprehensive study of the current scenario to safeguard the trends and prospects of the market. Bioinformatics Software Research reports also track future…

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Problem with phylotype(taxonomy=final.taxonomy) – Commands in mothur

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…

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Using mothur toolsuite on Galaxy to analyze microbial datasets : bioinformatics

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…

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The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold

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…

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16s rRNA Sequencing Meta-analysis Reconstruction Tool (using mothur).

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…

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Skin microbiome composition & diversity in Atopic dermatitis

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…

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Clustering in virome

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…

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Bug#984243: Help: mothur: ftbfs with GCC-11

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…

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The Profile and Function of Gut Microbiota in Diabetic Nephropathy

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…

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[Solved] tatements are true about the commands used in mothur during the process of generating contigs, filtering and merging the contigs and countin…

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…

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deseq2 tutorial microbiome

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…

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Mother update request – Galaxyproject/Tools-Iuc

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…

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Add ASV/OTU to taxonomy string for sequences

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

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