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This line https://github.com/biocore/biom-format/blob/master/biom/table.py#L241 is passing as `shape=(len(md),)`. However, if each element in `md` is a list, it will fail with this error:
```
biom co…
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I like the dada2 approach and I think it greatly enhances how we evaluate NGS data.
I understand how the dada2 algorithm makes unsupervised "OTUs"/sequence variants or whatever we call them. The pr…
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@gavinhuttley has suggested that we call it the SHARK.
@gregcaporaso seems naturally apprehensive.
How about the following backronym?
SHort read tAxonomy Rating for Classifiers?
So it would be SHA…
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Hi Ben,
Thanks for excellent tools and troubleshooting! I have paired end samples with 2*125bp. I used split_libraries_fastq command in QIIME with quality score 19 to demultiplex samples. The Blas…
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Here is the list of unique studies (and their starting row numbers in the db) that do not have initials in the Entered_By field.
```
> goo
row Common_Name …
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It seems like CREST or LCACLASSIFIER (it seems like your product uses two names interchangeably) uses the "silvamod" database by default. If I go to your user guide, the link to the page that describe…
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[assign_err.zip](https://github.com/karel-brinda/ProPhyle/files/521813/assign_err.zip)
Most of the reads are assigned to the last sequence in index.fa, which is the rightmost node in the taxonomic tre…
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Hello Jon!
Thanks a lot for UFITS, I find it very useful and user-friendly!
I would like to propose to make the input OTU table (`-i` or `--otu_table` flags) optional in `ufits taxonomy`. The hybrid …
vmikk updated
7 years ago
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I was wondering if you had information on how to interpret the output. I can understand that the first column is the sequence identifier, and the second column is the taxa assignment. The third is _p…
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Good morning,
First, thank you for the organization and capacity of CONCOCT- its been a very easy and fun tool to use! I have a question about following up on the complete example. I have 5 samples (…