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 ...
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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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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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kraken2 output to OTU table

I did run kraken2 on the 16s rRNA sample. I get two kinds of out put 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 ...
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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 so what i see is in each barcode file i have 1960 fastq files which i have merged. The i did trim the fastq files using ...
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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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