Schema for modENCODE CAGE Read Density - modENCODE CAGE Read Density for Different Developmental Stages

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Schema for modENCODE CAGE Read Density - modENCODE CAGE Read Density for Different Developmental Stages

Database: dm6 Primary Table: modE_Kc167_Cytoplasm_CTSS_plus Row Count: 1 Data last updated: 2022-10-21

field	example	SQL type	info
`fileName`	/gbdb/dm6/bbi/modENCODE_CAG...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/dm6/bbi/modENCODE_CAGE/Kc167_Cytoplasm_CTSS_normalized_plus.bw

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

modENCODE CAGE Read Density (tss_modECAGE) Track Description


	Description These tracks show the normalized density of CAGE reads from different developmental stages of D. melanogaster. The CAGE datasets were produced by the modENCODE project and were obtained from the NCBI Sequence Read Archive database under the accession number SRP001602. Methods Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. The alignment results were analyzed by CAGEr. The tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters: `method = "powerLaw", fitInRange = c(10, 1000), alpha = 1.05, T = 110^6` Credits Hoskins RA, et al.* Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011 Feb;21(2):182-92. Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res. 2015 Apr 30;43(8):e51.