Schema for Combined modENCODE CAGE TSS - Combined Transcription Start Sites Identified by modENCODE CAGE

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Schema for Combined modENCODE CAGE TSS - Combined Transcription Start Sites Identified by modENCODE CAGE

Database: dm6 Primary Table: modECAGE_Combined_minus 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/modENCODE_CAGE_Combined_minus.bw

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

Combined modENCODE CAGE TSS (tss_modECAGE_Combined) 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. Consensus promoters across all the samples were produced by the consensusClusters function in CAGEr with the following parameters: `tpmThreshold = 5, qLow = 0.1, qUp = 0.9, maxDist = 100` 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.