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

Database: dm6 Primary Table: tss_modECAGE_Peaks Row Count: 14,110 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	7491	`int(10) unsigned`	range
`chromEnd`	7515	`int(10) unsigned`	range
`name`	0_0	`varchar(255)`	values
`score`	0	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	7491	`int(10) unsigned`	range
`thickEnd`	7515	`int(10) unsigned`	range
`reserved`	16711680	`int(10) unsigned`	range

This table points to a file in BigWig format.

Sample Rows

bin	chrom	chromStart	chromEnd	name	strand	thickStart	thickEnd	reserved
585	chr2L	7491	7515	0_0	+	7491	7515	16711680
585	chr2L	54856	54934	0_0	+	54856	54934	16711680
585	chr2L	55013	55069	0_0	+	55013	55069	16711680
585	chr2L	59230	59269	1_2	-	59230	59269	11177813
585	chr2L	67042	67044	3_0	+	67042	67044	65280
585	chr2L	71740	71741	1_2	+	71740	71741	11177813
585	chr2L	72597	72617	3_2	+	72597	72617	255
585	chr2L	87376	87400	2_0	-	87376	87400	5614080
585	chr2L	94720	94770	3_1	+	94720	94770	32896
585	chr2L	102381	102436	3_1	+	102381	102436	32896

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.

Description