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  • SeqTroubles
    Member
    • Sep 2016
    • 20

    #1

    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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