Entrez efetch bulk download into separate files

Create a free Team What is Teams? Collectives on Stack Overflow. Learn more. Alternative to Bio. Asked 5 years, 6 months ago. Active 5 years, 5 months ago. Viewed times. MattDMo If it is only one genome, why not manually download it from the FTP server ftp.

Thanks for the link! When you say you have unique ID numbers, are these GI or accession numbers? Additionally, I am assuming that you want to download the fasta files -- can you confirm if that is the case. Thanks for the reply cer! Yes, I want fasta files.

The ID number is called a "genome ID. Ive searched the genome db multiple ways and get links and ID numbers, but not an accession number for genome sequence in the Nucleotide database. Does such an accession even exist?

There are accession numbers for scaffolds within genomes for example LN Is that the best I can get? Melissa, I am not familiar with this genome ID. However, if you were amenable, you could do an NCBI nucleotide database search using terms that fit your criteria, and then download the resulting list of accession numbers. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name.

Email Required, but never shown. Featured on Meta. Reducing the weight of our footer. Now live: A fully responsive profile. Related 1. Hot Network Questions. Question feed. Renesh Bedre 1 minute read. Generate a gene counts matrix when featureCounts run separately on individual aligned files. Renesh Bedre 3 minute read. Renesh Bedre 5 minute read. The Entrez programming utilities E-utilities are a set of server-side programs and helps to download various biomedical data including nucleotide and protein sequences, molecular structures.