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Hi Everyone,
I am a beginner on metagenome binning.
Following the instructions, I am preparing my own R data sets.
In the file "rRNA.sh", the "16S.fa" could be generated, however the generation…
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We are planning to benchmark a set of metabarcoding tools and I thought to use OPAL. When investigating the tool, I thought one could use it for metabarcoding assessment just as well as long as one ca…
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Hello there!
I've been testing the VIRify v2.0 and I realised that the taxonomic annotation on the GFF file has the ranks inverted.
For instance:
taxonomy=Entomopoxvirinae;Poxviridae;Chitovira…
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Hi,
I generate a phyloseq file following the Bioconductor Workflow for Microbiome Data Analysis (https://f1000research.com/articles/5-1492/v2). Tree construction was done using dada2 and phangorn p…
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Hi!
I'm using the 16S-wf in the Epi2Me desktop application. I typically have full 16S reads and use the NCBI database that is provided in the workflow and minimap2 to assign taxonomy at species leve…
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Dear All,
I would like to know is there any option we can use user generated database instead of the default one? I would like to use rrNDB database. https://rrndb.umms.med.umich.edu/static/download/…
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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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Hello,
I have a dataset sequenced with Novaseq 6000 with 250PE for 77 libraries and four primers: 12S, COI, ITS and 18S, which gave ~1-6 million paired reads per library, with some lower exceptions…
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Thanks for sharing the protocol. I have tried it for some prophage genomes, but most genomes can only have the taxonomic information in "class" level. Is there a way to get species/family level inform…
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Hello Gert-Jan,
I am working on the same COI metabarcoding project mentioned before, but now encountering some issues with incorporating in-house generated barcodes. The in-house barcode database i…