Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
NCBI taxid download Pol8 Bioinformatics 3 01-29-2015 09:04 AM
How to download gene annotation from NCBI? jgarbe Bioinformatics 9 01-14-2015 11:26 AM
batch download from NCBI FTP Zapages General 1 07-26-2014 10:22 AM
How to download all the bacterial protein data from NCBI? kaiwang Bioinformatics 3 08-14-2013 10:45 PM
How to download gene annotation for influenza from NCBI? taro.ishibash Bioinformatics 0 11-08-2012 03:21 PM

Thread Tools
Old 12-09-2017, 05:17 AM   #1
Location: Ireland

Join Date: Sep 2016
Posts: 20
Default Download sequences from NCBI and eDirect

Hi All,

I want to down load a batch of sequences from NCBI using eDirect.

I currently using the follow command which

esearch -db nuccore -query "escherichia coli" | efilter -source refseq -molecule rna | efetch -format fasta | xargs -n 1 sh -c 'efetch -db nuccore -id "$0" -format fasta > "$0".fna'

But this seem to spit out each individual line as a fasta.

How to I get the command to give me individual files for each strain.

SeqTroubles is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:00 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO