Difference between revisions of "Rnaseq library details"
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== Model == | == Model == | ||
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Latest revision as of 16:46, 9 January 2014
Contents
Model
/////////////////////////////////////////////////////////////////////////////////// // // ?Rnaseq_library class - gw3 Jan 2014 // Holds details of the Experiment (SRX*) RNASeq libraries in the Short Read Archive // /////////////////////////////////////////////////////////////////////////////////// ?Rnaseq_library Title Text // summary of this library Abstract Text // description of the study Species UNIQUE ?Species Condition ?Condition // this contains details of the organism used DB_info Database ?Database ?Database_field UNIQUE ?Accession_number // the various SRA and GEO IDs for this data Submitting_lab Text // name of the submitting lab, e.g. UWGS-RW Preparation Library_source Text // GENOMIC / TRANSCRIPTOMIC etc. Library_selection Text // cDNA / RANDOM / size fractionation etc. Library_strategy Text // RNA-Seq / WGS / EST / ChIP-Seq etc. Ribozero // Ribo-zero treated to reduce the amount of ribosome gene transcripts Library_name Text // name given by the authors e.g. EE_ce1003_rw005 Stranded // stranded reads (as opposed to unstranded r Paired_end Len Int Standard_dev Int // Paired end layout details Length then Stadard deviation (as opposed to Single end layout) Instrument_platform Text Instrument_model Text Quality_score UNIQUE PHRED SOLEXA // Solexa format prior to Illumina version 1.3 (in version 1.3 and later PHRED is used by Illumina) Reference ?Paper XREF Rnaseq_library BAM Assembly Text // WormBase assembly that the data was aligned to Run Text ?Database ?Database_field UNIQUE ?Accession_number // the accession of the BAM files produced from the Run files in this library Ignore Text // reason why this library should not be used in the RNASeq pipeline Remark Text #Evidence // add this to ?Paper ?Paper Refers_to Rnaseq_library ?Rnaseq_library XREF Reference #Evidence
Suggestions
Condition XREF