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

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

Database: DobsGB1 Primary Table: adultfemales_rnaseqcov Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/DobsGB1/bbi/modENCODE...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/DobsGB1/bbi/modENCODE_RNASeq/DobsGB1_Whole_Female.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. obscura RNA-Seq reads against the D. obscura DobsGB1 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 BioProject accession number PRJDB4576. References Nozawa M, Onizuka K, Fujimi M, Ikeo K, Gojobori T. Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. Nat Commun. 2016 Nov 29;7:13659. 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.