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Hello all.
We have extracted DNA from tomato leaves and roots. The DNA was amplified using the 16S primers 515f/806r and ITS primers gITS7/ITS4 (ITS2 region). We used PNA clamps with the 16S PCRs to …
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I'm processing our first Element AVITI 16S amplicon sequencing data, using dada2 in QIIME2. I'm wondering how to do this optimally, as it appears that it behaves a bit differently from MiSeq data in d…
mniku updated
3 months ago
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@benjjneb
Hi,
I used to manipulate MiSeq reads on Qiime2 where I can use DADA2 plugins along with other q2-plugins easily. I need to export the sequence data as fasta file collapsed at specific t…
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Hello and thank you for your great work, I've been using dada2 for more than 2 years now and it's amazing.
Currently I am working with human gut 16s V3-V4 250+250 sequencing data. The dataset inclu…
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Thank you for creating such a great tool.
I have one question, your tool doesn't seem to generate the gene count matrix directly. If I want to generate a count table in addition to gene presence abs…
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Hi developer,
I came across an issue when I tried to run Canu on the server. Error reported as follow. Any suggestions?
Looking forward to hearing back from you, many thanks!
Wengang
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## Short description of the problem
I end up with different results per sample when I run co-assembly on all my samples at once vs going through the anvio pipeline for subsets of my files.
## an…
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Hi,
I'm trying to use singlem to assess the percentage of eukaryotes in a metagenome. For this I have generated an artificial metagenome derived from known fungal and bacterial genomes. I have enco…
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I am looking for a tool to do assembly to assembly mapping for bacteria and I am very excited to have found minimap2!
Do you have a best practices document for this use case?
Or is `minimap2 -a…
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I'm planning on using your wonderful Salmon tool v0.12.0 for generating TPM counts with a view to quantifying relative abundance of certain bacterial antibiotic resistance genes in my shotgun (human g…