Description
These tracks show the interquantile widths of the promoters based on CAGE data for
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
The promoter widths were determined by the cumulativeCTSSdistribution and quantilePositions functions in CAGEr
using the following parameters:
clusters = "tagClusters", qLow = 0.1, qUp = 0.9
Display Conventions
The span of each feature corresponds to the promoter width. The thin box within each span corresponds to
the interquantile width (qLow = 0.1 to qUp = 0.9) that captures 80% of the CAGE signal. The thicker box
denotes the position within the promoter with the highest CAGE signal.
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.
|