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The RDP classifier wrapper in assign_taxonomy.py does not print taxonomic assignments for sequences that are too short for taxonomy assignment with RDP. These raise a ShortSequenceException and are sk…
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I tested the taxonomic assignment script on a very small test sample with the MOTHUR classifier and it produces an error.
The offending command is the following:
```
assign_taxonomy.py -i rep_set.f…
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What we actually are going to present at IWBBIO? Metapasta or MG7?
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Goal 2 from Kseniia's list, mentioned in https://github.com/ropensci/RNeXML/issues/21#issuecomment-25735531
Will be a good example for the manuscript, once gov't shutdown ends and the taxize servers…
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Hi Joey,
suggestion for consideration rather than bug.
Sometimes if I label OTUs on a plot using Genus there are labels missing due to that particular taxonomic level being absent for that OTU. In…
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Also, filter new OTUs to a new-only OTU table, summarize taxa, and define how many of these new OTUs are uncharacterized at the phylum level, at the class level, ...
this is similar to this:
http://w…
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Hi,
I was willing to use Phyloseq to visualize some metagenomics results from our project MG7 ( https://github.com/pablopareja/MG7 ).
I've been having a look at the Biom format http://biom-format.org…
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Hi,
I'm trying to import data from QIIME using import_qiime or import_biom. Here are the versions I'm using, my code and the errors:
QIIME version: MacQIIME 1.7.0-20130523
R version: R version 3.0.2…
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Hi,
I have been trying to make some basic figures with phyloseq. I have first subsetted my data to the top 10 most common OTUs
TopNOTUs
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I tested the taxonomic assignment script on a very small test sample with the RDP classifier and it produces an empty file as output. Inspecting with `top` you can see the RDP java processes run for a…