-
Hello everyone,
I am trying to run pan-genome analysis on 32 AOA species using the full genebanks I obtained from the NCBI and this code
./panX.py -fn data/genebanks -sl pratice -t 6
Howeve…
-
Hello everyone,
I am trying to download the standard Kraken2 database and I'm having issues with the rsync_from_ncbi_.pl file. Here is my terminal input and the resulting output and error:
**Inp…
-
## Sept 26, 2024
@natefoo started the process:
- Galaxy dbKeys will be set to GenBank or RefSeq IDs (`assembly version ID` column in https://brc-analytics.org/data/organisms)
- Names (in tool dropdo…
-
When trying out the script with bcbio-gff 0.7.0 and biopython 1.81 I get the following error:
```py
python ~/code/GFF-to-GenBank/gff_to_genbank_edit.py results/genome_annotation.gff3 data/referenc…
-
Hi,
I want to annotate a Verticillium Genome via command line. I installed augustus and all neccesary stuff to get it work and tested with the example data -> worked.
My Verticillium Genome is als…
-
Sorry if I missed something, but is there a command line tool for updating an existing annotation with promoter sequences? Say I have a Genbank annotation through NCBI's annotation pipeline and I wan…
-
I am trying to find the accessions to Rep, MOB and MPF genes identified by mob-typer in NCBI. An example would be an identified Rep protein: 002374__CP004064_00076. When I search for this accession in…
-
E.g. if the label is 'Rana sp. nov. G12345', look up G12345 in our genbank table to get appropriate SILVA or NCBI taxon, and suggest that taxon. (which we hope is not 'Rana sp. nov.')
-
I would like to extract the translated orfs after running a translated search (proteins against nucleotide) and `gff2db` followed by `translatenucs` seemed like the way to go. However, MMseqs2 has bee…
-
When running 01_perform_dda.snakefile and downloading a query genome for `Muribaculaceae bacterium Z82` from genbank with the [dominating set differential abundance](https://github.com/dib-lab/2022-do…