These tracks show the interquantile widths of the promoters for D. melanogaster
based on the Exo-seq data collected at different Zeitgeber Times (ZT) and temperatures. The Exo-seq datasets were obtained from the NCBI Sequence Read Archive database under the accession number SRP045351.
Each dataset was mapped to the D. melanogaster release 6 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 = 1.16, 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
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.
Afik S, Bartok O, Artyomov MN, Shishkin AA, Kadri S, Hanan M, Zhu X, Garber M, Kadener S.
Defining the 5′ and 3′ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. Nucleic Acids Res. 2017 Jun 20;45(11):e95.
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.