CapSeq Tag Clusters Track Settings
CapSeq Tag Clusters for w1118 (wildtype) Ovaries   (All Expression and Regulation tracks)

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Data last updated at UCSC: 2022-10-21


These tracks show the interquantile widths of the promoters for D. melanogaster based on the CapSeq data for Drosophila adult ovaries (genotype w1118.tm3). The CapSeq datasets were obtained from the NCBI Sequence Read Archive database under the accession number SRP103849.


Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. Only the alignments with mapping quality of 5 or above are kept. 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 CapSeq signal. The thicker box denotes the position within the promoter with the highest CapSeq signal.


Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 2007 Mar 23;128(6):1089-103.

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.