Tag: OTU

Community succession and functional prediction of microbial consortium with straw degradation during subculture at low temperature

Changes of straw degradation characteristics at different culture stages Corn straw degradation ratio Corn straw weight loss in M44 at F1 reached 35.90% at 15 ℃ for 21 days, which was greater than that at F5, F8, and F11 by 2.33%, 3.01%, and 3.35%, respectively. There were no significant differences between…

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How to make alpha diversity boxplot?

How to make alpha diversity boxplot? 1 How to make alpha diversity boxplot? I am trying to perform alpha diversity and I performed scatter plot for shannon measure,How can I make boxplot?? meta.physeq = sample_data(meta) tax <- otu_table(tax,taxa_are_rows=FALSE) physeq.alpha = phyloseq(ASV, tax, meta.physeq) sample_data(physeq.alpha)$shannon.physeq <- estimate_richness(physeq.alpha, measures=”Shannon”) plot_richness(physeq.alpha, measures=”Shannon”) alpha_diversity…

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GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

GWAS identifies genetic variations associated with agronomic traits in foxtail millet A total of 827 foxtail millet cultivars collected from China were sequenced and genotyped using common single-nucleotide polymorphisms (SNPs) based on a ~423 Mb Setaria italica cv. Zhanggu reference genome (v.2.3)27. In total, 161,562 SNPs were detected after stringent steps…

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phyloseq – R: How can I fix an as.matrix() error message?

I am trying to create a taxonomic reference for some 16S/18S data in R and have been running into issues when following this tutorial. I am trying to create an OTU table from a taxonomy/sequence table that was bootstrapped for only 18S data. Here is the error I receive and…

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KEGG T01003: 286761

Entry 286761            CDS       T01003                                  Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1   KO K11861   deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno  Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:rno01002]    286761 (Vcpip1)  09182 Protein families: genetic information processing   04121 Ubiquitin system [BR:rno04121]    286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.19  Omega peptidases    3.4.19.12  ubiquitinyl…

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Index of /~psgendb/doc/pkg/cd-hit-v4.8.1-2019-0228/doc

Name Last modified Size Description Parent Directory   –   Figure1.png 2015-05-05 00:44 43K   Figure2.png 2015-05-05 00:44 42K   Figure3.png 2015-05-05 00:44 129K   Figure4.png 2015-05-05 00:44 30K   cd-hit-est.man 2020-06-16 12:13 5.6K   cd-hit-otu-miseq-Fig..> 2017-03-25 12:00 117K   cd-hit.man 2020-06-16 12:12 4.4K   cdhit-user-guide.pdf 2017-05-01 11:52 412K  …

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Metagenomics technology and microbial community diversity analysis methods

A large number of microorganisms in nature cannot be cultivated under laboratory conditions by pure culture methods, and the technical methods of traditional microbiology limit the research on environmental microorganisms. The rapid development of high-throughput omics technology has enabled humans to have an unprecedented understanding of the complex microbial communities…

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r – phyloseq: Discrepancies in otu counts before and after using tax_glom

Maybe I missed something in how tax_glom works but as I did not find any info here nor elsewhere on the web, maybe someone here can help. I do not provide data but I can on request. Here is the code highlighting the issue I have CYANO_gen <- CYANO %>%…

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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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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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How to pool phyloseq data?

How to pool phyloseq data? 0 @688ee615 Last seen 1 day ago United Kingdom I hope someone can help. I am trying to carry out some differential abundance analysis on some microbiome data that has come from a metabarcoding experiment using 16S illumina sequencing. I have processed my data using…

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ggplot2 – Fail to plot by group on a phyloseq object generated by R package Divnet

Once you already have your phyloseq object df_family, you can use the function estimate_richness from phyloseq. You can then join the sample meta data to this data frame of alpha diversities. Finally, you can use ggplot2 directly to customize your plot accordingly, e.g. to put different sample groups (here SampleType)…

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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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Issues removing unwanted taxa from phyloseq object

Hi everyone, I am currently in the process of removing unwanted taxa (Kingdom=”Eukaryota”, Family=”Mitochondria”, and Order=”Chloroplast”) from a phyloseq object I created. This phyloseq object was created using my outputs from DADA2 (OTU table, taxonomy table, and metadata file). I have saved a taxonomy table in CSV format at every…

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Gene Set – TFDP2

Symbol Name ACBD6 acyl-CoA binding domain containing 6 ACO2 aconitase 2, mitochondrial ADAMTS2 ADAM metallopeptidase with thrombospondin type 1 motif, 2 AK2 adenylate kinase 2 ALDH6A1 aldehyde dehydrogenase 6 family, member A1 AP1S1 adaptor-related protein complex 1, sigma 1 subunit AP4M1 adaptor-related protein complex 4, mu 1 subunit APH1A APH1A…

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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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combine OTU and tax table and replace actual sequences with OTU ids (Phyloseq/dada2)

This is to the part of the question “replace actual sequences with OTU ids (Phyloseq/dada2)?” I contacted the phyloseq/dada2 developers and based on Susan Holmes’ reply (github.com/joey711/phyloseq/issues/1030) I came up with this piece of code to replace the amplicon sequences with a numbered OTU header. Further discussion can be found…

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ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples | BMC Microbiology

1. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9. PubMed  PubMed Central  CAS  Google Scholar  2. Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A…

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Circos plot of dominant OTU with phylogenetic tree

Circos plot of dominant OTU with phylogenetic tree 0 I am trying to create a circos plot of dominant OTUs (from metagenomic data) with a phylogenetic tree inside the circle and the heatmaps around (like the attached image). Kindly suggest how can I achieve this using circos. Thank you. analysis…

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Network plot using NetCoMi and igraph

Hi, I am trying to plot the Network plot as suggested here (github.com/stefpeschel/NetCoMi#single-association-network-on-genus-level) by using igraph and NetCoMi. But I am not getting the network plot as expected- I just want to label the hub genera and phyla. and want the network plot in spherical layout. # Agglomerate to genus…

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How to remove the header in fasta file and keep only the desirable part on ubuntu?

How to remove the header in fasta file and keep only the desirable part on ubuntu? 2 Hi all, I have a fasta file with this header >10005_M12.fastq Otu0001|242290|M1.fastq-M12.fastq-M5.fastq-URTM6.fastq-M7.fastq-M9.fastq I want to remove all the header parts except the OTU (with its number), I used the this command “sed ‘s/>M.Otu/>Otu/g’…

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How to remove the header in fasta file and keep only the desirable part on ububtu?

How to remove the header in fasta file and keep only the desirable part on ububtu? 1 Hi all, I have a fasta file with this header >10005_M12.fastq Otu0001|242290|M1.fastq-M12.fastq-M5.fastq-URTM6.fastq-M7.fastq-M9.fastq I want to remove all the header parts except the OTU (with its number), I used the this command “sed ‘s/>M.Otu/>Otu/g’…

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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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Basic logic and use of PERMANOVA for microbiome data

Basic logic and use of PERMANOVA for microbiome data 1 PERMANOVA is frequently used in microbiome studies when analyzing beta diversity. While I know that basics of PERMANOVA are similar to ANOVA (with some differences related to permutation), I have a hard time understanding the logic of this analysis in…

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