Combined modENCODE CAGE TSS Track Settings

Combined Transcription Start Sites Identified by modENCODE CAGE (All Expression and Regulation tracks)

Maximum 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: -100000 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 views (Help):

Peaks ▾

Signals ▾

Peaks Configuration Show only items with score at or above: (range: 0 to 1000)

List subtracks: only selected/visible all
	hide	modENCODE CAGE Peaks	TSS Identified by Combined modENCODE CAGE	Schema
	hide Configure	modENCODE CAGE (Plus)	Combined modENCODE CAGE Read Density (Plus Strand)	Schema
	hide Configure	modENCODE CAGE (Minus)	Combined modENCODE CAGE Read Density (Minus Strand)	Schema

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.