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

Display mode:       Reset to defaults   

Type of graph:
Track height: pixels (range: 11 to 110)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: -100000 to 100000)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
Select subtracks by strand and condition: (help)
 All Strand Plus  Minus 
Condition
Control 
Exosome RNAi 
List subtracks: only selected/visible    all  
 
hide
 Configure
 Control (+)  CAGE Read Density for Control Sample (Plus)   Schema 
 
hide
 Configure
 Control (-)  CAGE Read Density for Control Sample (Minus)   Schema 
 
hide
 Configure
 Exosome RNAi (+)  CAGE Read Density for Exosome RNAi Sample (Plus)   Schema 
 
hide
 Configure
 Exosome RNAi (-)  CAGE Read Density for Exosome RNAi Sample (Minus)   Schema 

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.