Combined modENCODE CAGE TSS Track Settings

Combined Transcription Start Sites Identified by modENCODE CAGE (All Expression and Regulation tracks)

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	hide	CAGE Peaks	TSS Identified by Combined modENCODE CAGE	Schema
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Description

These tracks show the normalized density of CAGE reads from 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. Consensus promoters across all the samples were produced by the consensusClusters function in CAGEr with the following parameters:


tpmThreshold = 5, qLow = 0.1, qUp = 0.9, maxDist = 100

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.