Question: Download all NCBI gene names, synonyms, and gene ID for an organism
0
gravatar for Patrick
2.0 years ago by
Patrick0
Patrick0 wrote:

I would like to download all NCBI genes, synonyms and gene ID #s for mouse, and then human. Ive tried downloading lists of gene names, and then searching NCBI to get gene ID, however I run into problems with NCBI having a different official name compared to what I input. Is there a way to get all of the gene IDs easily in one go? Thanks!

gene • 3.5k views
ADD COMMENTlink modified 2.0 years ago by Istvan Albert ♦♦ 81k • written 2.0 years ago by Patrick0
1
gravatar for skbrimer
2.0 years ago by
skbrimer560
United States
skbrimer560 wrote:

Do you mean, you would like to download the complete reference from NCBI from the RefSeq FTP site?

like here for mouse and her for human

ADD COMMENTlink written 2.0 years ago by skbrimer560

I am only looking for a table or list. Something along the lines of:
Symbol Entrez Gene ID
Pzp 11287
Aanat 11298
Aatk 11302
Abca1 11303
Abca4 11304

(That has all Gene IDs)

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Patrick0
1

Quite straightforward. For Mus musculus gene: go to the NCBI gene page >> https://www.ncbi.nlm.nih.gov/gene/?term=Mus+musculus and go to "send to" >> file >> tabular (text). Then open the file and select the column 3 and 6 and save to new table:

cat gene_result.txt  | cut -f3,6 > Mus_mus_gene_id.txt
ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by lessismore710

Wow, that was too easy. Exactly what I was looking for, Thank you!

ADD REPLYlink written 2.0 years ago by Patrick0
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