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Old 12-09-2017, 05:17 AM   #1
SeqTroubles
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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.

Thanks
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