How to limit sequences downloaded from NCBI to published data only

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4.9 years ago

sbombin ▴ 10

I want to download reference sequences of 28S from NCBI for taxonomic identification of my data. I know that I need to use "Entrez ESearch" to download data. However, I cannot find a way to limit the downloaded data to sequences that have been published in the past. The meta data for sequences that I want to exclude have label "Unpublished" in Journal row.

I tried such command but it did not work esearch -db nuccore -query "28S AND ulva [ORGN]" | efilter -query "NOT Unpublished [JOUR]" | efetch -format fasta

esearch reference sequences next-gen NCBI • 855 views

ADD COMMENT • link 4.9 years ago by sbombin ▴ 10

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Can you post an example of where you are seeing the "unpublished" label in journal row?

ADD REPLY • link 4.9 years ago by GenoMax 141k

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Did you find a solution? Other than filtering after searching.

ADD REPLY • link 3.6 years ago by salix • 0

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