Questions tagged [microbial-genomics]
The microbial-genomics tag has no usage guidance.
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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 ...
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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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1
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Get a comprehensive list of virulence factors for certain or all pathogens?
Is there a database with all known proteins/genes of specific pathogens such as Staph aureus and annotated whether it is a known virulence or resistance factor that idealy can be downloaded in table ...
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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 ...
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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 ...
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Regarding canonical analysis of principal coordinates (CAP) for linking microbial data with elements
I used the below code to do CAP analysis to link microbial data with elements, but not sure how to do statistical analysis to show which element variation is responsible most for the difference in ...
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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 ...
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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 ...
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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. ...
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kraken2 to OTU table creation
I did run kraken2 and I get two kinds of output
How do I generate OTU table from these outputs for phyloseq usage?
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error in random forest analysis
I am now struggling to do random forest analysis, I will be thankful if you could help with code for random forest analysis.
I got samples from the root, soil, and leaf from two regions (bau & mau)...
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156
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repophlan script to download bacterial genome
I am trying to donwload the microbial genome using the repophlan_get_microbes.py (https://github.com/SegataLab/repophlan) but now it is running more than 10 days and still not finished on slurm HPC.
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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 ...
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120
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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 ...
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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 ...
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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 ...
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Optimum parameters for genome assembly via canu
I have been trying to assemble my genome via canu. Canu gave me about 200 contigs using default parameters. My genomesize is ~9Mbp. Can you recommend some parameters I can tweak to decrease the ...
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where to find pathogenicity metadata for E.coli genomes
I have a list of about 900 E.coli genome ids (Genbank plus NCTC ids), e.g.:
...
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