Combined Exo-seq TSS Track Settings

Combined Transcription Start Sites Identified by Exo-seq (All Expression and Regulation tracks)

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	hide	Exo-seq Peaks	TSS Identified by Combined Exo-seq	Schema
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Description

These tracks show the normalized density of the combined Exo-seq reads from D. melanogaster 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.

Methods

Each dataset was mapped to the D. melanogaster release 6 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

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.