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

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

Database: DereCAF1 Primary Table: adultmales_rnaseqcov Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/DereCAF1/bbi/modENCOD...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/DereCAF1/bbi/modENCODE_RNASeq/DereCAF1_Whole_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. erecta RNA-Seq reads against the D. erecta DereCAF1 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 PRJNA264407 (ovarian follicle cells; Chirn GW 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. Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. PLoS Genet. 2015 Nov 20;11(11):e1005652. 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.