Schema for TSRchitect Combined RAMPAGE TSS - TSRchitect Combined RAMPAGE Transcription Start Sites

Database: DereCAF1 Primary Table: tss_RAMPAGE2_star_Peaks Data last updated: 2019-07-06
Big Bed File: /gbdb/DereCAF1/bbi/RAMPAGE2_star/DereCAF1_tsrchitectPeaks.bb
Item Count: 15,579
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	scaffold_1134	Reference sequence chromosome or scaffold
`chromStart`	178	Start position in chromosome
`chromEnd`	179	End position in chromosome
`name`	tsr_peaked_7	Name of RAMPAGE peak
`score`	1000	Score from 0-1000
`strand`	+	+ or -
`nTSSs`	1	Count of TSSs
`nTAGs`	37	Count of tags
`tsrPeak`	1	Maximum tag count fraction for all TSS positions in the TSR
`tsrWdth`	1	Width of TSR
`tsrTrq`	0	TSR torque; measure of TSR balance
`tsrSI`	2	Shape index (SI) value of TSR
`tsrMSI`	1	Modified shape index (MSI) value of TSR

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	nTSSs	nTAGs	tsrPeak	tsrWdth	tsrTrq	tsrSI	tsrMSI
scaffold_1134	178	179	tsr_peaked_7	1000	+	1	37	1	1	0	2	1
scaffold_1134	508	520	tsr_peaked_8	690	+	2	259	0.69	12	-2.1	1.11	0.11

TSRchitect Combined RAMPAGE TSS (tss_RAMPAGE2_star_Combined) Track Description


	Description This track shows the locations of putative Transcription Start Sites (TSS) in the D. erecta genome based on the analysis of RAMPAGE results from multiple developmental stages of D. erecta embryos. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE89304. The RAMPAGE reads were mapped against the D. erecta (DereCAF1) assembly using STAR. The putative promoter regions were identified by TSRchitect. References Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. Batut PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6.

Description

References