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

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

Database: DsecCAF1 Primary Table: adultfemales_rnaseqcov Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/DsecCAF1/bbi/modENCOD...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/DsecCAF1/bbi/modENCODE_RNASeq/DsecCAF1_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. sechellia RNA-Seq reads against the D. sechellia DsecCAF1 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 numbers PRJNA205470 (adult females; McManus CJ et al., 2014) and PRJNA414017 (adult males; Ma S et al., 2018). References Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN. Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity. Aging Cell. 2018 Apr 19:e12740. McManus CJ, Coolon JD, Eipper-Mains J, Wittkopp PJ, Graveley BR. Evolution of splicing regulatory networks in Drosophila. Genome Res. 2014 May;24(5):786-96. 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.