Schema for RNA-Seq Coverage (Tissues) - RNA-Seq Coverage for Different Tissues

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Schema for RNA-Seq Coverage (Tissues) - RNA-Seq Coverage for Different Tissues

Database: DanaCAF1 Primary Table: SRP058321_male_carcass_coverage Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/DanaCAF1/bbi/rnaseq/S...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/DanaCAF1/bbi/rnaseq/SRP058321_Dana_male_carcass.bw

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

RNA-Seq Coverage (Tissues) (DanaCAF1_tissues_rnaseq) Track Description


	Description These tracks show the RNA-Seq coverage for different D. ananassae tissues. The RNA-Seq read coverage was normalized by a wigsum of 100,000,000 (1 million 100bp reads). The RNA-Seq reads were mapped against the D. ananassae DanaCAF1 genome assembly using HISAT2. RNA-Seq reads from multiple replicates were combined together. The read coverage tracks were produced by the bam2wig.py program in RSeQC. The RNA-Seq data were retrieved from the NCBI Sequence Read Archive using the BioProject accession numbers PRJNA257286 and PRJNA388952. References Yang H, Jaime M, Polihronakis M, Kanegawa K, Markow T, Kaneshiro K, Oliver B. Re-annotation of eight Drosophila genomes. Life Sci Alliance. 2018 Dec 24;1(6):e201800156. Rogers RL, Shao L, Sanjak JS, Andolfatto P, Thornton KR. Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group. G3 (Bethesda). 2014 Oct 1;4(12):2345-51. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357-60. Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012 Aug 15;28(16):2184-5.