modENCODE CAGE Read Density Track Settings

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modENCODE CAGE Read Density for Different Tissues (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: 0 to 100000)
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 tissue: (help)

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Gender:

List subtracks: only selected/visible all ()
	hide Configure	Female Carcass (+)	modENCODE CAGE Read Density for Female Carcass (Plus)	Schema
	hide Configure	Female Carcass (-)	modENCODE CAGE Read Density for Female Carcass (Minus)	Schema
	hide Configure	Ovaries (+)	modENCODE CAGE Read Density for Female Ovaries (Plus)	Schema
	hide Configure	Ovaries (-)	modENCODE CAGE Read Density for Female Ovaries (Minus)	Schema
	hide Configure	Male Carcass (+)	modENCODE CAGE Read Density for Male Carcass (Plus)	Schema
	hide Configure	Male Carcass (-)	modENCODE CAGE Read Density for Male Carcass (Minus)	Schema
	hide Configure	Testes (+)	modENCODE CAGE Read Density for Male Testes (Plus)	Schema
	hide Configure	Testes (-)	modENCODE CAGE Read Density for Male Testes (Minus)	Schema

Description

These tracks show the normalized density of CAGE reads from different tissues of D. pseudoobscura. 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. pseudoobscura DpseGB3 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 = 1*10^6

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.