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

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

Database: DyakCAF1 Primary Table: adultmales_rnaseqcov Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/DyakCAF1/bbi/modENCOD...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/DyakCAF1/bbi/modENCODE_RNASeq/DyakCAF1_Whole_Dyak_261.01_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. yakuba RNA-Seq reads (generated by the modENCODE project) against the D. yakuba DyakCAF1 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 SRP006203. References Chen ZX et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul;24(7):1209-23. 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.