Combined MachiBase TSS Track Settings

Combined MachiBase Transcription Start Sites (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	MachiBase Peaks	TSS Identified by Combined MachiBase Results	Schema
	hide Configure	MachiBase (Plus)	Combined MachiBase Read Density (Plus Strand)	Schema
	hide Configure	MachiBase (Minus)	Combined MachiBase Read Density (Minus Strand)	Schema

Description

These tracks show the normalized density of SAGE reads from different developmental stages of D. melanogaster. The datasets were produced by MachiBase and were obtained from the NCBI BioProject database under the accession number PRJNA79391.

Methods

Each dataset was mapped to the D. melanogaster release 6 assembly using bwa and 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

Ahsan B, Saito TL, Hashimoto S, Muramatsu K, Tsuda M, Sasaki A, Matsushima K, Aigaki T, Morishita S. MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. Nucleic Acids Res. 2009 Jan;37(Database issue):D49-53.

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.