how to download all reference files with ensembl and taxon ID?
1
0
Entering edit mode
9 months ago

Hello,

I would like to download all the reference sequences of viruses deposited. I remember this could be done with esearch/efetch and the taxon ID of the species of interest (I believe viruses have ID 10239).

I am trying with:

esearch -db taxonomy -query 10239 | efetch -format=fasta > ref.fa

but I am not getting anything.

What would be the correct syntax?

Thank you

sequence ensembl efetch esearch • 307 views
ADD COMMENT
0
Entering edit mode
9 months ago

I have found it:

esearch -db "nucleotide" -query "txid10239 [Organism] AND refseq[filter]" | efetch -format fasta > ref.fa

Case closed.

ADD COMMENT

Login before adding your answer.

Traffic: 1618 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6