gene-id
download a gene dataset by NCBI Gene ID
datasets download gene - download a gene dataset
datasets download gene [flags]
Download a gene data package including gene, transcript and protein sequence, a data table and a data report. Gene data packages can be specified by NCBI Gene ID, symbol or RefSeq accession. Data packages are downloaded as a zip file.
The default gene dataset includes the following files:
Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.
datasets download gene gene-id 672
datasets download gene symbol brca1 --taxon mouse
datasets download gene accession NP_000483.3
datasets download gene gene-id 2778 --fasta-filter NC_000020.11,NM_001077490.3,NP_001070958.1
--api-key string NCBI Datasets API Key
--exclude-gene exclude gene.fna (gene sequence file)
--exclude-protein exclude protein.faa (protein sequence file)
--exclude-rna exclude rna.fna (transcript sequence file)
--fasta-filter strings limit gene fasta download to a specific list of accessions
--fasta-filter-file string file of accessions to limit gene fasta download
--filename string specify a custom file name for the downloaded dataset (default "ncbi_dataset.zip")
-h, --help help for gene
--include-3p-utr include 3p_utr.fna (3'-UTR sequence file)
--include-5p-utr include 5p_utr.fna (5'-UTR sequence file)
--include-cds include cds.fna (CDS sequence file)
--no-progressbar hide progress bar
download a gene dataset by NCBI Gene ID
download a gene dataset by gene symbol
download a gene dataset by RefSeq nucleotide or protein accession
download a gene dataset by taxon