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Link Sequencing project accession number to published paper

Is there a way to find the paper or papers that were published with data from a submitted sequencing project in SRA or ENA?

I downloaded some sequences but I cannot for the life of me remember the paper I got it from (very stupid of me) I have done some analysis and I would like to compare it to their findings.

ena sra
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updated by GenoMax GenoMax • written by son_of_7less • son_of_7less

Was that successful? If not check the fastq headers. These might contain the accession number and this should link to some NCBI entries with the reference.

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written by ATpoint ATpoint

1 answer

Using Entrezdirect (example replace your own SRA#):

$ esearch -db sra -query  SRR1448774 | elink -target pubmed | esummary | xtract -pattern DocumentSummary -element FullJournalName,ELocationID
Genome research doi: 10.1101/gr.181883.114
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written by GenoMax GenoMax

This is the output I get. Even when with the same ID in your code.

curl: (3) URL using bad/illegal format or missing URL ERROR: curl command failed ( Wed 13 Jul 16:03:22 GMT 2022 ) with: 3 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?query_key=1&WebEnv=MCID_62ceecc944e839595d19905e&retstart=0&retmax=1&db=sra&rettype=uilist&retmode=text&tool=edirect&edirect=16.2&edirect_os=Linux&email=%%20has%20address%20 WARNING: FAILURE ( Wed 13 Jul 16:03:22 GMT 2022 ) nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -query_key 1 -WebEnv MCID_62ceecc944e839595d19905e -retstart 0 -retmax 1 -db sra -rettype uilist -retmode text -tool edirect -edirect 16.2 -edirect_os Linux -email "@ has address EMPTY RESULT

SECOND ATTEMPT curl: (3) URL using bad/illegal format or missing URL ERROR: curl command failed ( Wed 13 Jul 16:03:24 GMT 2022 ) with: 3 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?query_key=1&WebEnv=MCID_62ceecc944e839595d19905e&retstart=0&retmax=1&db=sra&rettype=uilist&retmode=text&tool=edirect&edirect=16.2&edirect_os=Linux&email=%%20has%20address%20 WARNING: FAILURE ( Wed 13 Jul 16:03:23 GMT 2022 )

nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -query_key 1 -WebEnv MCID_62ceecc944e839595d19905e -retstart 0 -retmax 1 -db sra -rettype uilist -retmode text -tool edirect -edirect 16.2 -edirect_os Linux -email "@ has address agmay" EMPTY RESULT

LAST ATTEMPT curl: (3) URL using bad/illegal format or missing URL ERROR: curl command failed ( Wed 13 Jul 16:03:25 GMT 2022 ) with: 3 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?query_key=1&WebEnv=MCID_62ceecc944e839595d19905e&retstart=0&retmax=1&db=sra&rettype=uilist&retmode=text&tool=edirect&edirect=16.2&edirect_os=Linux&email=%%20has%20address%20 ERROR: FAILURE ( Wed 13 Jul 16:03:25 GMT 2022 )

nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -query_key 1 -WebEnv MCID_62ceecc944e839595d19905e -retstart 0 -retmax 1 -db sra -rettype uilist -retmode text -tool edirect -edirect 16.2 -edirect_os Linux -email "@ has address agmay" EMPTY RESULT

QUERY FAILURE curl: (3) URL using bad/illegal format or missing URL ERROR: curl command failed ( Wed 13 Jul 16:03:27 GMT 2022 ) with: 3 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?query_key=1&WebEnv=MCID_62ceecc944e839595d19905e&retstart=0&retmax=1&db=sra&rettype=uilist&retmode=text&tool=edirect&edirect=16.2&edirect_os=Linux&email=%%20has%20address%20 ERROR: ELink failure ERROR: Missing -db argument

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written by son_of_7less • son_of_7less

How did you install Entrezdirect? Using conda or otherwise? This looks like a local failure of some sort on your side.

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written by GenoMax GenoMax

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