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
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.
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