Download RunInfo Table from command line
0
1
Entering edit mode
4.6 years ago

I am trying to download the RunInfo Table for a number of entries in the BioProject or SRA databases. I have installed Entrez Direct and have esearch and efetch working, but they don't provide the same information as downloading the RunInfo Table manually.

When I run this code:

esearch -db sra -q 'PRJNA417256' | efetch -format runinfo > PRJNA417256.sra.csv

I get a .csv with the following fields:

  • 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

When I manually download the RunInfo Table I get a .csv with the following fields:

  • Run
  • Antibody
  • Assay Type
  • AvgSpotLen
  • BioProject
  • BioSample
  • cell_line
  • Center Name
  • Consent
  • DATASTORE filetype
  • DATASTORE provider
  • DATASTORE region
  • Experiment
  • GEO_Accession
  • Instrument
  • LibraryLayout
  • LibrarySelection
  • LibrarySource
  • MBases
  • MBytes
  • Organism
  • Platform
  • ReleaseDate
  • sample_acc
  • Sample Name
  • source_name
  • SRA Study
  • transfection
  • treatment

Is there a way to get the contents of the RunInfo Table from the command line (particularly: Antibody, Assay Type, cell_line, Organism, source_name, transfection, treatment)?

Thanks.

Entrez Direct NCBI • 1.7k views
ADD COMMENT

Login before adding your answer.

Traffic: 2387 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6