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Questions tagged [16rrna]

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I want to know what are the main differences between two R Objects constructed for analysis of microbiome data: phyloseq and TreeSummarizedExperiment

I am looking for main differences between two R Objects constructed for analysis of microbiome data: phyloseq object and TreeSummarizedExperiment object First, I will provide a little information ...
akspat's user avatar
  • 13
1 vote
1 answer
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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 ...
Laura's user avatar
  • 909
2 votes
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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 ...
Geomicro's user avatar
  • 121
1 vote
1 answer
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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 ...
Laura's user avatar
  • 909
0 votes
1 answer
39 views

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 ...
Mohamed Samir's user avatar
2 votes
2 answers
178 views

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/...
Freezing Soul's user avatar
2 votes
2 answers
66 views

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 ...
Julieta's user avatar
  • 21
2 votes
1 answer
73 views

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, ...
raysteven's user avatar
4 votes
1 answer
94 views

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 ...
h3ab74's user avatar
  • 836
1 vote
1 answer
1k views

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 ...
h3ab74's user avatar
  • 836
1 vote
1 answer
599 views

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 ...
h3ab74's user avatar
  • 836