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## Links to resources that I'm finding that are related to my goal: BLAST transcriptome to get taxonomy info at the phylum, order, class, level and to exclude mammals
### Need general help with und…
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Hi, I am trying to use CAMISIM to simulate metagenome. I tried using the docker version and got the following error:
$ docker run -it cami/camisim:latest metagenome_from_profile.py -c sp_config.ini
…
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I just mapped 0.5mil 150bp HiSeq reads from a human gut metagenome (previously profiled with kraken2; looked very normal for the sample time) to RefSeq-bacteria, and I'm getting the following output:
…
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I'm building a new accessionTaxa.sql db with protein accessions and get the following error:
> library(taxonomizr)
> getNamesAndNodes()
trying URL 'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.t…
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Just checked, and the latest NCBI taxonomy dump (September 2019) is essentially unchanged from Jan 2019 for the *oomycetes*:
```
$ diff names-2019-01.dmp names-2019-09.dmp
9,11c9,11
< 2759 | eu…
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Hi Rich,
I launched the viewer by activating the blobtools2 conda environment and then `blobtools host hs_Omyriophila/`. I can see the dataset when I write "all" in the query field. I can even see …
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### Describe your issue
Hello,
I'm confused regarding the exact purpose/use case of taxid-changelog.
Would I want to run the following:
```
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxd…
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Hello,
I just installed pantagruel and trying the minimal test.
I ran the initialisation :
```
./pantagruel_pipeline/pantagruel/pantagruel -d testPTGdatabase -r ./ -f PANTAGFAM -I s.raguidea…
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Hi,
i downloaded data via genome_updater
```
$ Tools/genome_updater/genome_updater.sh -g "taxids:1386" -d "refseq" -l "Chromosome" -f "genomic.fna.gz,assembly_report.txt" -t 36 -o References/al…
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Hello there,
I would like to know if there is anyway to download data from other species than this list : "archae bacteria fungi protozoa viral" ?
For specific purpose, I would like to construct…