Questions tagged [16rrna]
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Using average of sequence similarities when delimiting genera - how to deal with outliers?
Sometimes I am trying to see where a (bacterial) genus ends and where another one begins based on 16S rRNA phylogenies. Of course, the length and support of the branch matter a lot, but this question ...
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otu_table from phyloseq object does not have correct abundance: all asv are "0" for specific group of samples
This question was also asked on stack overflow
I have QIIME2 outputs (feature table, tree, taxonomy, and metadata) that I've imported into R using qiime2R (v. 0.99.6) ‘qza_to_phyloseq’ to create a ...
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Variation in 16S rRNA between assemblers - how do I know which is real?
I have a low-diversity metagenome (~11 bins > 80% completion). Out of the bins, 3 are of interest to me. None of the lower-completion bins that can be identified are from the group of interest. So ...
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome
Cross-posted on biostars: https://www.biostars.org/p/9572744/
I am trying to understand better what number to be used and how to put it in the function MRcoefs within the Metagenomeseq package in R ...
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Automated method to figure out whether a recognition site is conserved or not using the results of simulated restriction digestion
Restrict from EMBOSS Suit version 6.3.1 with the following
parameters: snucleotide1, sitelen = 4, rformat = table, enzymes =
enzymes.txt.
From the 4379 enzymes present in REBASE, we selected the 650 ...
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How do i search by these gene properties in NCBI's GenBank?
I want to search GenBank entries by gene product and taxon id.
Taking the 16s rRNA as an example for a gene and Piscirickettsia salmonis (taxon:1238) for a taxon:
https://www.ncbi.nlm.nih.gov/nuccore/...
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WCGNA - Relate modules with Y features when the % of variance explained of each eigengen is low
I'm doing a WCGNA analysis (signed network) on microbiome 16S data.
I have transformed counts to centeres log-ratio transformed data (CLR) to address the compositional characteristics of the data and ...
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Questions about microbial 16s rRNA phylogenetic, ANI Taxonomy, and GGDC
I have a few questions about these three methods.
We commonly use 16s rRNA to identify species and construct a phylogenetic tree. If there's a new isolate from a new and undiscovered ecosystem, ...
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Co-occurrence networks in Metagenomics studies
I have recently acquired some 16S metagenomics data, and was wondering if anyone can speak of the potential limitations, challenges as well as advantages to conducting a network-based study on ...
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Searching for adapter sequences in FASTQ files - metgenomics
I have recently received some metagenomic data from 16S rrna sequencing. The sequencing company claim to have removed primers, however not adapter sequences. Please note that the files have been ...
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maxEE parameter from DADA2 package in R
I have just started the QC steps from the dada2 pipeline, and have failed to find a detailed explanation of what the maxEE argument entails.
I have surfed many forums, as well as the details given by ...
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