CapSeq Read Density Track Settings
CapSeq Read Density for w1118 (wildtype) Ovaries   (All Expression and Regulation tracks)

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 Ovaries (Plus)  CapSeq of Adult Ovaries (Plus)   Schema 
 Ovaries (Minus)  CapSeq of Adult Ovaries (Minus)   Schema 


These tracks show the normalized density of CapSeq reads 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


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.