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Questions tagged [microbial-genomics]

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How can I use statistics to compare microbial phenotypes?

Note: this question has also been asked on Biostars I am currently trying to create a theoretical argument that a microbe's phenotype can affect gene expression in their host. I have 5 species of ...
pythonbeginner44's user avatar
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Kraken2 > OTU format > Phyloseq

A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION. I would like to make a tree if the data using a ...
Reebola95's user avatar
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Model optimization causes overfitting

I'm working on an ML model to predict colorectal cancer using data from the human microbiome (collected from fecal samples). My dataset is made up of metadata (containing phenotypic information on the ...
user17818805's user avatar
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When to use Ariba vs Roary or other genomics tools to call drug-resistance variants?

I have a large dataset of assemblies of bacterial S. aureus genomes (~1000, same species). I am looking at different tools to estimate the presence of drug-resistance factors such as blaZ or ampC. ...
Soerendip's user avatar
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How to compare Log2 Fold Change values

I have 5 sets of Log2 Fold Change values pulled off DualSeqDB. Each of the 5 groups corresponds to a different microbial taxon. Within the 5 groups, there are many Log2 Fold Change values, each ...
pythonbeginner44's user avatar
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How to extract certain genes including non-coding regions?

I would like to look at the non-coding regions of some genes. I have around 1000 full genome assemblies and I was able to extract the nucleotide sequences for certain proteins with ...
Soerendip's user avatar
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Analyzing and visualizing metagenomic data

I am starting out in metagenomics, Aim I wish to understand the whole analysis from the raw reads to interpretation. Background My current pipeline is used for: analyzing human gut microbiota cleans ...
Roger V.'s user avatar
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Nanopore microbiome data analysis 16s rRNA data

The steps I have done so far: used guppy to do base calling from fast5 to fastq. In each barcode file I have 1960 fastq files which I have merged. trimmed the fastq files using NanoFilt Now what I ...
kcm's user avatar
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Alternatives to phrap for merging contigs with overlapping ends?

I have bins from metagenomes generated with metabat2 on bitbucket/berkleylab/scr which are predicted as viral by MARVEL. MARVEL ...
Stanley Ho's user avatar
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Looking for guidance on Microbial Association Networks (MANs) Inference with samples from different metagenomics/metatranscriptomics studies

I'm Sebastian, working on my MSc thesis, aiming to create a knowledge graph of the wastewater treatment microbiome. We're using Netcomi for constructing Microbial Association Networks (MANs) from ...
Sebastian Ayala's user avatar
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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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kraken2 output to OTU table

I ran kraken2 on a 16s rRNA sample. I get two kinds of output, one like this and the other one like this. So I have many files like this for each sample of my control and test group. How do I generate ...
kcm's user avatar
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