Get data and information
Time: 20 min
Objectives: Be able to upload data needed.
Prerequisites: You should have access to the GALAXY platform and be familiar with basic navigation within it.
Connect to your galaxy account.
Download Genome Assembly Data
To make it simple we will work on a single genome assembly file, but the same steps can be applied to multiple files if needed. I offer you the choice to use the assembly of your choice among a list of Escherichia coli assemblies Accession.The accesion number uniquely identifies a genome assembly in public databases.
| Accession | URL |
|---|---|
| GCA_964200045.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/964/200/045/GCF_964200045.1_366_BP0076U_scaffolds/GCF_964200045.1_366_BP0076U_scaffolds_genomic.fna.gz |
| GCA_964200025.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/964/200/025/GCF_964200025.1_372_BP0083B_scaffolds/GCF_964200025.1_372_BP0083B_scaffolds_genomic.fna.gz |
| GCA_964200035.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/964/200/035/GCF_964200035.1_368_BP0078U_scaffolds/GCF_964200035.1_368_BP0078U_scaffolds_genomic.fna.gz |
| GCA_964200015.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/964/200/015/GCF_964200015.1_323_BP0014P_scaffolds/GCF_964200015.1_323_BP0014P_scaffolds_genomic.fna.gz |
| GCA_964199995.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/964/199/995/GCF_964199995.1_364_BP0073U-1_scaffolds/GCF_964199995.1_364_BP0073U-1_scaffolds_genomic.fna.gz |
| GCA_964200005.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/964/200/005/GCF_964200005.1_327_BP0021B_scaffolds/GCF_964200005.1_327_BP0021B_scaffolds_genomic.fna.gz |
Click on the “Upload Data” button in Galaxy to open the upload interface
.Then click on “Paste/Fetch Data” to open the interface where you can paste the URLs of the genome assemblies you want to upload.
- Now 1) provide a file name ; 2) paste the URLs of the genome assemblies you want to upload into the provided text area ; 3) click on start to begin the upload process.
=> As a result you should see the uploaded genome assembly files listed in your Galaxy history on the right side of the interface:
Get taxonomical information
This step is for sure only possible if you know what organism your genome assembly belongs to.
Go the NCBI Taxonomy website.
We are currenlty working with Escherichia coli, so you can search for “Escherichia coli”.
Lineage (full): cellular organisms; Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia; Escherichia coli
A taxonomy ID is a unique identifier assigned to each organism in the NCBI Taxonomy database. The Taxonomy ID of Escherichia coli is 562.