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Hello,
at first, I would like to thank you for dada2. I try to analyze microbiome of soil samples using this software and I have found some problems. Therefore, I would like to ask you for some advi…
JoBrz updated
5 years ago
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Hi everyone!
Recently I was working on a huge amount of 16S amplicon data from various environments. It is not a surprise that in some (most of...) samples the **unclassified** taxa (at least at genu…
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Hi,
I'm testing mOTUs2 with some mouse metagenomic data (cecum content). Do you have any plans to augment the existing database by other organisms (e.g. mouse) as well? The existing database works …
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Hi @schuyler-smith, I have a few more small requests for you to fix. Please look over this report:
```
✖ not use "Depends" in DESCRIPTION, as it can cause name
clashes, and poor interaction…
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Can you point me to a tutorial or accessor function for how to take an OTU table + metadata and convert this to a taxmap object, which can then be used to make plots? Is this possible with the package…
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Hey @reptalex,
I continue to try out phylofactor for 16S data. I build a tree by aligning the sequences for each OTU.
I run phlofactor on the raw counts, which gives me a number of interesting…
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Hi All,
I realize this is more of a chimera problem than a dada2 problem, though the dada2 approach results in many more sequences to check for chimeras than traditional clustering approaches. I am…
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Edited to reflect updated understanding of issue:
Labman expects the wet lab to put values from qiita.study_sample.sample_id into the platemap, but that the wet lab does not actually have those id…
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Hi,
I have been using metacoder to visualize core microbiome as no. of obs (otus), and now I would like to display the core as read count (abundance).
My otu_table is unfiltered, I mean it has non-s…
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