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annotate test-data/sra_manifest.tabular @ 36:1ec814014652 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cb858cbf5d9e307b663105f674f1acaa4f90a1fb
author iuc
date Thu, 14 Mar 2024 15:21:59 +0000
parents 248f85ff0733
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248f85ff0733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1e2492fa4557ddc6ffefc16b249ed9ef0207d5e1"
iuc
parents:
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1 Run Assay Type BioProject BioSample Center Name Consent DATASTORE filetype DATASTORE provider DATASTORE region Experiment Instrument LibraryLayout LibrarySelection LibrarySource Organism Platform Sample Name SRA Study Bytes ReleaseDate Library Name Collection_Date isolate AvgSpotLen Bases BioSampleModel Host geo_loc_name_country geo_loc_name_country_continent geo_loc_name host_disease collected_by isolation_source lat_lon host_sex passage_history strain host_age host_subject_id ENA-FIRST-PUBLIC (run) ENA-FIRST-PUBLIC ENA-LAST-UPDATE (run) ENA-LAST-UPDATE geographic_location_(country_and/or_sea) host_health_state collecting_institution collector_name geographic_location_(region_and_locality) host_common_name host_scientific_name gisaid_id isolation_source_host-associated sample_capture_status isolate (run) ARTIC_barcode_identifiers host_tissue_sampled library_id AssemblyName GEO_Accession (exp) source_name tissue barcode_identifiers Cell_type host_description sample_type age_event Age Biomaterial_provider cell_number cell_processing_protocol cell_quality disease disease_stage ETHNICITY health_state sex single_cell synthetic tissue_processing cell_subsets patient_group disease_state subject_status tissue/cell_type sample_origin organ host_disease_stage stock_production_date culture_collection COUNTRY Extraction-method host_disease_outcome identification_method Laboratory_Host link_addit_analys ref_biomaterial datatype (run)
248f85ff0733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1e2492fa4557ddc6ffefc16b249ed9ef0207d5e1"
iuc
parents:
diff changeset
2 SRR11953971 RNA-Seq PRJNA622837 SAMN14938999 BROAD INSTITUTE OF HARVARD AND MIT public bam,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 SRX8498148 Illumina NovaSeq 6000 PAIRED cDNA VIRAL RNA Severe acute respiratory syndrome coronavirus 2 ILLUMINA MA_MGH_00524 SRP266465 207470 2020-06-08T00:00:00Z SAMN14938999_ERCC-00040_RandomHexamer_NexteraXT 2020-03-17 not applicable 202 415514 Pathogen.cl Homo sapiens USA North America USA: Massachusetts COVID-19 Massachusetts General Hospital nasopharyngeal swab missing not applicable not applicable MA_MGH_00524