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During a search, the target sequences are sorted by decreasing k-mer composition similarity with the query sequence. The target sequences that are the most likely to get a high similarity score with t…
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#### Summary:
I'm trying to fetch some data from NCBI but it didn't work. Then, i try to use the example which is in the README. I got the same error.
#### Description:
I think it's a problem f…
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Hi Qiime,
I got the output from assign_taxonomy.py, and trying to make sense what it means for the 3rd and 4th columns. I read from http://qiime.org/scripts/assign_taxonomy.html, and learned that
>…
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This is a feature request.
Currently the taxonomy databases uses during `assignTaxonomy` are kept on Dropbox which requires a manual confirmation of the download (can not be downloaded by a script).…
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I have a valid JSON .biom file that cannot be written in HDF5 format due to its axis metadata. I've [attached a file](https://github.com/biocore/biom-format/files/490823/feature-table.txt) to reproduc…
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I am doing an ITS region fungal study. I used the usearch v8.1 pipeline, without any qiime scripts, to get me to the point of a biom table with taxonomic assignments. As far as I can tell, the json bi…
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Should this be happening in FIA_conversion-SGD_remove_dups.csv?
Note two different rows with spcd=241, 3 for spcd=800, 2 for spcd=693
Also Doug. fir is not given a PalEON taxon, which I guess makes …
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First off, thank you for creating and updating dada2. I am very excited by by your approach and am trying to build it into my lab's pipeline. I have however seen a few odd things and I think something…
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Dear Jennifer and ghost-tree team,
Is it possible to perform a phylogenetic placement of sequences on a ghost-tree (e.g., with [pplacer](http://matsen.fhcrc.org/pplacer/), [EPA](https://github.com/zha…
vmikk updated
7 years ago
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Hi Ben,
I'm finding that in my final taxa output object (I'm not sure how to call a DADA2 final output), several OTUs are repeated. For example, in my top 10 I have two methanosaeta and two smithella…