Exosome RNAi CAGE Track Settings
 
Exosome RNAi Knockdown CAGE TSS   (All Expression and Regulation tracks)

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Description

These tracks show the combined normalized density of CAGE reads for exosome-depleted and control samples from D. melanogaster S2 cells. The CAGE datasets were obtained from the NCBI Sequence Read Archive database under the accession number SRP131270.

Methods

Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. 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(500, 50000), alpha = 1.07, T = 1*10^6

References

Rennie S, Dalby M, Lloret-Llinares M, Bakoulis S, Dalager Vaagensø C, Heick Jensen T, Andersson R. Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. Nucleic Acids Res. 2018 Jun 20;46(11):5455-5469.

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.