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dada2 is great, thanks for sharing such a useful tool!
I have a confusing result where assignTaxonomy returns Eukaryote assignments for bacterial 16s sequences. I have seen Issue #70 and confirm…
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When I type (in RStudio):
`speciesSummary("American Black Duck", diet, by = "Order")`
I get this error message:
`Error in if (x[level] == "") { : missing value where TRUE/FALSE needed`
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this gives a violation, and looks odd as "unfolded protein response" is a signalling pathway
![check 2nd one](https://cloud.githubusercontent.com/assets/7359272/21583034/9c082c3e-d065-11e6-86…
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Add only in Plant (or organisms that do photosynthesis)
- [ ] GO:0042646 plastid nucleoid
- [ ] GO:0016028 rhabdomere
The following have “only in cellular organisms, but should be only in Met…
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```
dammit annotate Mspi_normalized_Trinity.fasta --busco-group metazoa --n_threads 36 --database-dir ~/mnt
/dammit/ --full
--- Running annotate!
Transcriptome file: Mspi_Rcorr_trin…
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The online databases cannot be located, probably due to a change in (the format of) the webpage:
> getBridgeNames()
> [1] "
drlrc updated
7 years ago
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All the TFs (to be used for TemplateReactionRegulation/controller) are there created as Rna rather than Protein, why?..
Sounds like a mistake.
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Hi
I am using Biopython 1.68 .
If I read in a file from NCBI that follows the Genbank format and write it out.
The DBLINK record seems to change the entries from having a space after the colon to…
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```
[~/mnt/dammit]$ dammit databases --install --database-dir ~/mnt/dammit --full --busco-group metazoa
========================================
dammit! a tool for easy de novo transcriptome annota…
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Distributor ID: Ubuntu
Description: Ubuntu 14.10
Release: 14.10
Codename: utopic
Followed instructions here - http://genomehubs.org/documentation/installing-docker/ and here https://easy-import.…