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12-09-2017, 05:17 AM
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Member
Location: Ireland Join Date: Sep 2016
Posts: 20
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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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