How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
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4 weeks ago
Harshita • 0

I am using some fungal isolates' whole genome sequences to reconstruct phylogeny with my isolates, but I am not able to find some SRA IDs for the isolates already used and published in other works. Is there any way I can know if the name of the submission is probably different from what I see on NCBI when I type, or if there is a way to find the SRA IDs of those sequences?

Refer to some IDs used in this publication: https://journals.asm.org/doi/10.1128/mbio.01219-17

SRA whole-genome-sequencing NCBI • 380 views
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4 weeks ago
GenoMax 143k

Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa

This table has the SRA# you need.


OR

Using EntrezDirect (only one record shown here, there are 45 total) :

$ esearch -db bioproject -query PRJNA320483 | elink -target sra | efetch -format runinfo
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
SRR14705994,2022-06-30 00:21:00,2021-06-02 01:53:15,23917379,7175213700,23917379,300,2603,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR014/14705/SRR14705994/SRR14705994.lite.1,SRX11043948,CpJA159_Lib,WGS,RANDOM,GENOMIC,PAIRED,0,0,ILLUMINA,Illumina HiSeq 2000,SRP322222,PRJNA320483,,320483,SRS9112198,SAMN19488802,simple,318829,Pyricularia oryzae,CpJA159,,,,,,,no,,,,,UNIVERSITY OF KENTUCKY,SRA1239061,,public,701E33E57A319359F5465FD8283FA279,D7F5EC84290C2D1B8D4259ED5677314F
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Thank you so much for helping me out in this!

I have used most of the sequences that are found in this table. But, some samples like these SAMN08009548, do not have SRA data. What can be done in that case?

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For those samples it appears that raw data was not submitted. Just an assembly.

$ esearch -db biosample -query SAMN08009548 | elink -target assembly | efetch -format docsum
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE DocumentSummarySet>
<DocumentSummarySet status="OK">
  <DbBuild>Build240520-1130.1</DbBuild>
  <DocumentSummary>
    <Id>1559091</Id>
    <GbUid>6007438</GbUid>
    <AssemblyAccession>GCA_002925295.1</AssemblyAccession>
    <LastMajorReleaseAccession>GCA_002925295.1</LastMajorReleaseAccession>
    <ChainId>2925295</ChainId>
    <AssemblyName>ASM292529v1</AssemblyName>
    <Taxid>318829</Taxid>
    <Organism>Pyricularia oryzae (rice blast fungus)</Organism>
    <SpeciesTaxid>318829</SpeciesTaxid>
    <SpeciesName>Pyricularia oryzae</SpeciesName>
    <AssemblyType>haploid</AssemblyType>
    <AssemblyStatus>Scaffold</AssemblyStatus>
    <AssemblyStatusSort>6</AssemblyStatusSort>
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It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the SRA IDs. I think that these have a different name in the database, and that's why I cannot find them.

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