TSRchitect RAMPAGE TSS Read Density Track Settings

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TSRchitect RAMPAGE Read Density for Different Developmental Stages (All Expression and Regulation tracks)

Display mode: Reset to defaults

Type of graph:
Track height:	pixels (range: 11 to 110)
Data view scaling:	Always include zero:
Vertical viewing range:	min:	max: (range: -10000 to 10000)
Transform function:	Transform data points by:
Windowing function:		Smoothing window:	pixels
Negate values:
Draw y indicator lines:	at y = 0.0: at y =

Graph configuration help

Select subtracks by strand and stage: (help)

All	*Strand*	Plus	Minus
*Stage*
Embryos 1hr
Embryos 2hr
Embryos 3hr
Embryos 4hr
Embryos 5hr
Embryos 6hr
Embryos 7hr
Embryos 8hr
Embryos 9hr
Embryos 10hr
Embryos 11hr
Embryos 12hr
Embryos 13hr
Embryos 14hr
Embryos 15hr
Embryos 16hr
Embryos 17hr
Embryos 18hr
Embryos 19hr
Embryos 20hr
Embryos 21hr
Embryos 22hr
Embryos 23hr
*Stage*
All	*Strand*	Plus	Minus

Select subtracks further by: (select multiple categories and items - help)

StageGroup:

List subtracks: only selected/visible all ()
	hide Configure	Embryos, 1 hr (Plus)	RAMPAGE Read Density for 1 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 1 hr (Minus)	RAMPAGE Read Density for 1 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 2 hr (Plus)	RAMPAGE Read Density for 2 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 2 hr (Minus)	RAMPAGE Read Density for 2 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 3 hr (Plus)	RAMPAGE Read Density for 3 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 3 hr (Minus)	RAMPAGE Read Density for 3 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 4 hr (Plus)	RAMPAGE Read Density for 4 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 4 hr (Minus)	RAMPAGE Read Density for 4 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 5 hr (Plus)	RAMPAGE Read Density for 5 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 5 hr (Minus)	RAMPAGE Read Density for 5 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 6 hr (Plus)	RAMPAGE Read Density for 6 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 6 hr (Minus)	RAMPAGE Read Density for 6 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 7 hr (Plus)	RAMPAGE Read Density for 7 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 7 hr (Minus)	RAMPAGE Read Density for 7 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 8 hr (Plus)	RAMPAGE Read Density for 8 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 8 hr (Minus)	RAMPAGE Read Density for 8 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 9 hr (Plus)	RAMPAGE Read Density for 9 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 9 hr (Minus)	RAMPAGE Read Density for 9 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 10 hr (Plus)	RAMPAGE Read Density for 10 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 10 hr (Minus)	RAMPAGE Read Density for 10 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 11 hr (Plus)	RAMPAGE Read Density for 11 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 11 hr (Minus)	RAMPAGE Read Density for 11 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 12 hr (Plus)	RAMPAGE Read Density for 12 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 12 hr (Minus)	RAMPAGE Read Density for 12 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 13 hr (Plus)	RAMPAGE Read Density for 13 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 13 hr (Minus)	RAMPAGE Read Density for 13 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 14 hr (Plus)	RAMPAGE Read Density for 14 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 14 hr (Minus)	RAMPAGE Read Density for 14 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 15 hr (Plus)	RAMPAGE Read Density for 15 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 15 hr (Minus)	RAMPAGE Read Density for 15 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 16 hr (Plus)	RAMPAGE Read Density for 16 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 16 hr (Minus)	RAMPAGE Read Density for 16 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 17 hr (Plus)	RAMPAGE Read Density for 17 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 17 hr (Minus)	RAMPAGE Read Density for 17 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 18 hr (Plus)	RAMPAGE Read Density for 18 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 18 hr (Minus)	RAMPAGE Read Density for 18 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 19 hr (Plus)	RAMPAGE Read Density for 19 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 19 hr (Minus)	RAMPAGE Read Density for 19 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 20 hr (Plus)	RAMPAGE Read Density for 20 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 20 hr (Minus)	RAMPAGE Read Density for 20 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 21 hr (Plus)	RAMPAGE Read Density for 21 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 21 hr (Minus)	RAMPAGE Read Density for 21 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 22 hr (Plus)	RAMPAGE Read Density for 22 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 22 hr (Minus)	RAMPAGE Read Density for 22 hr Embryo (Minus)	Schema
	hide Configure	Embryos, 23 hr (Plus)	RAMPAGE Read Density for 23 hr Embryo (Plus)	Schema
	hide Configure	Embryos, 23 hr (Minus)	RAMPAGE Read Density for 23 hr Embryo (Minus)	Schema

Description

These tracks show the density of RAMPAGE reads from different 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.

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.