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If in the sample sheet an entry for the `Sample_Project` is not matching our predefined values `Antibodies/Metagenomics/Plasmids/Resistance/Other`, it should automatically be assigned to the project `…
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**references**
- White JR, Nagarajan N, Pop M (2009). [Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples](http://www.ploscompbiol.org/article/info%3Ado…
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Hi,
Thanks for such useful tool!
I've been following your Example 03: Metagenomic application - Metagenomic analysis of the Ethiopian cohort, but I got stuck in the least section of drawing heatmaps…
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Is there a simple script available in python or R to get all of the data as a biom table and tsv with matching sample indices?
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### Description of bug
I can't seem to figure out what the problem is. I am not sure what I should do about the no-saved checkpoints. The warning message reads as follows.
warning.log (below)
…
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## Background
GBIF has recently begun publishing records from a metagenomics publisher MGnify.
https://www.gbif.org/publisher/ab733144-7043-4e88-bd4f-fca7bf858880
Typically these records can b…
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[InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains](https://www.biorxiv.org/content/10.1101/2020.01.22.915579v1)
Coexisting mi…
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Hello,
We want to run krakenuniq for datasets containing 100-200 samples of about 25-30M reads each.
As of now, **we are not able to successfully complete one run**, even when trying to use only…
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Hello, I am quantifying the abundance of genes in metagenomics data using paired-end reads (R1 and R2). I used --meta flag according to the salmon manual and provided R1 and R2 of each sample. Howeve…
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I used the Bulk download script (https://github.com/ProteinsWebTeam/ebi-metagenomics/wiki/Downloading-results-programmatically) to download metagenomes per project (ProcessedReads fasta files) and it …