Tag: OTU

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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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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