Exo-seq Read Density Track Settings
 
Exo-seq Read Density at Different Zeitgeber Times and Temperatures   (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: 0 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 zt: (help)
 All Strand Plus  Minus 
ZT
zt3 
zt9 
zt15 
zt23 
Select subtracks further by: (select multiple categories and items - help)
Temperature:

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 Configure 		 zt3 temp_18C (+)  Exo-seq Read Density for Zeitgeber Time 3 at 18C (Plus)   Schema 
 
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 Configure 		 zt3 temp_18C (-)  Exo-seq Read Density for Zeitgeber Time 3 at 18C (Minus)   Schema 
 
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 Configure 		 zt9 temp_18C (+)  Exo-seq Read Density for Zeitgeber Time 9 at 18C (Plus)   Schema 
 
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 Configure 		 zt9 temp_18C (-)  Exo-seq Read Density for Zeitgeber Time 9 at 18C (Minus)   Schema 
 
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 Configure 		 zt15 temp_18C (+)  Exo-seq Read Density for Zeitgeber Time 15 at 18C (Plus)   Schema 
 
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 Configure 		 zt15 temp_18C (-)  Exo-seq Read Density for Zeitgeber Time 15 at 18C (Minus)   Schema 
 
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 Configure 		 zt23 temp_18C (+)  Exo-seq Read Density for Zeitgeber Time 23 at 18C (Plus)   Schema 
 
hide
 Configure 		 zt23 temp_18C (-)  Exo-seq Read Density for Zeitgeber Time 23 at 18C (Minus)   Schema 
 
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 Configure 		 zt3 temp_25C (+)  Exo-seq Read Density for Zeitgeber Time 3 at 25C (Plus)   Schema 
 
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 Configure 		 zt3 temp_25C (-)  Exo-seq Read Density for Zeitgeber Time 3 at 25C (Minus)   Schema 
 
hide
 Configure 		 zt9 temp_25C (+)  Exo-seq Read Density for Zeitgeber Time 9 at 25C (Plus)   Schema 
 
hide
 Configure 		 zt9 temp_25C (-)  Exo-seq Read Density for Zeitgeber Time 9 at 25C (Minus)   Schema 
 
hide
 Configure 		 zt15 temp_25C (+)  Exo-seq Read Density for Zeitgeber Time 15 at 25C (Plus)   Schema 
 
hide
 Configure 		 zt15 temp_25C (-)  Exo-seq Read Density for Zeitgeber Time 15 at 25C (Minus)   Schema 
 
hide
 Configure 		 zt23 temp_25C (+)  Exo-seq Read Density for Zeitgeber Time 23 at 25C (Plus)   Schema 
 
hide
 Configure 		 zt23 temp_25C (-)  Exo-seq Read Density for Zeitgeber Time 23 at 25C (Minus)   Schema 
 
hide
 Configure 		 zt3 temp_29C (+)  Exo-seq Read Density for Zeitgeber Time 3 at 29C (Plus)   Schema 
 
hide
 Configure 		 zt3 temp_29C (-)  Exo-seq Read Density for Zeitgeber Time 3 at 29C (Minus)   Schema 
 
hide
 Configure 		 zt9 temp_29C (+)  Exo-seq Read Density for Zeitgeber Time 9 at 29C (Plus)   Schema 
 
hide
 Configure 		 zt9 temp_29C (-)  Exo-seq Read Density for Zeitgeber Time 9 at 29C (Minus)   Schema 
 
hide
 Configure 		 zt15 temp_29C (+)  Exo-seq Read Density for Zeitgeber Time 15 at 29C (Plus)   Schema 
 
hide
 Configure 		 zt15 temp_29C (-)  Exo-seq Read Density for Zeitgeber Time 15 at 29C (Minus)   Schema 
 
hide
 Configure 		 zt23 temp_29C (+)  Exo-seq Read Density for Zeitgeber Time 23 at 29C (Plus)   Schema 
 
hide
 Configure 		 zt23 temp_29C (-)  Exo-seq Read Density for Zeitgeber Time 23 at 29C (Minus)   Schema 
    

Description

These tracks show the normalized density of 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. The tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters:

method = "powerLaw", fitInRange = c(10, 1000), alpha = 1.16, T = 1*10^6

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.