Schema for RNA-Seq Coverage - D. grimshawi RNA-Seq Read Coverage

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Schema for RNA-Seq Coverage - D. grimshawi RNA-Seq Read Coverage

Database: DgriCAF1 Primary Table: adultmales_rnaseqcov Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/DgriCAF1/bbi/modENCOD...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/DgriCAF1/bbi/modENCODE_RNASeq/DgriCAF1_Whole_Dgri_G1_Male.bw

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RNA-Seq Coverage (rnaseq_coverage) Track Description


	Description This track was created by mapping D. grimshawi RNA-Seq reads against the D. grimshawi DgriCAF1 assembly using HISAT2. The RNA-Seq read coverage tracks were produced by the genomecov subprogram in bedtools. The RNA-Seq data were obtained from the NCBI Sequence Read Archive under the accession number SRP073087. References The RNA-Seq data were produced as part of the BioProject PRJNA317989: Expression profiling Hawaiian Drosophila species, tissues, and sexes. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements Nat Methods. 2015 Apr;12(4):357-60. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2.