Questions tagged [edirect]

Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments

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Linking GenBank records to biosamples (and vice versa) using edirect

Assume that I wish to find all complete human mitochondrial genome records on GenBank (or rather, NCBI nuccore) that also have an entry in NCBI's Biosample database. ...
Michael Gruenstaeudl's user avatar
3 votes
2 answers

efetch multiple records at once

If I want to efetch two records, I can do the following: efetch -db nuccore -id AB610939,AB610940 -format fasta I have hundreds of records to fetch. Can I put all ...
Supertech's user avatar
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No common application protocol between the client and server? An error when using Entrez Direct

After a long time not running EDirect, I got an error when I tried using it. It said," curl: schannel: next InitializationSecurityContext failed: Unknown error (0×80090367) - There is no common ...
Tinnhow Wung's user avatar
2 votes
1 answer

Default placeholder for missing fields doesn't work with block in xtract tool

I am using the xtract tool of the Entrez Direct (EDirect) package of NBCI. I have a list of Accession Numbers: ...
Rossy Clair's user avatar
3 votes
2 answers

NCBI - edirect suite to download all genome sequences associated with a query - troubleshooting

Not sure if this is allowed but I cannot think of a better place to ask. I am attempting to download all genomic sequences from refseq associated with the query Peptostreptococcaceae. I have been been ...
AudileF's user avatar
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