CSHL RAMPAGE TSS Read Density Track Settings
 
CSHL RAMPAGE Read Density for Different Developmental Stages   (All Expression and Regulation tracks)

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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 stage: (help)
 All Strand Plus  Minus 
Stage
Adult Female 
Embryo 
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Replicate:

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 Configure 		 Adult Females Replicate 1 (Plus)  RAMPAGE Read Density for Replicate 1 of Adult Females Sample (Plus)   Schema 
 
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 Configure 		 Adult Females Replicate 1 (Minus)  RAMPAGE Read Density for Replicate 1 of Adult Females Sample (Minus)   Schema 
 
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 Configure 		 Adult Females Replicate 2 (Plus)  RAMPAGE Read Density for Replicate 2 of Adult Females Sample (Plus)   Schema 
 
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 Configure 		 Adult Females Replicate 2 (Minus)  RAMPAGE Read Density for Replicate 2 of Adult Females Sample (Minus)   Schema 
 
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 Configure 		 Embryos Replicate 1 (Plus)  RAMPAGE Read Density for Replicate 1 of Embryos Sample (Plus)   Schema 
 
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 Configure 		 Embryos Replicate 1 (Minus)  RAMPAGE Read Density for Replicate 1 of Embryos Sample (Minus)   Schema 
 
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 Configure 		 Embryos Replicate 2 (Plus)  RAMPAGE Read Density for Replicate 2 of Embryos Sample (Plus)   Schema 
 
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 Configure 		 Embryos Replicate 2 (Minus)  RAMPAGE Read Density for Replicate 2 of Embryos Sample (Minus)   Schema 
    

Description

These tracks show the density of RAMPAGE reads from D. ananassae mixed embryos and adult females samples. The RAMPAGE reads were mapped against the D. ananassae (DanaRefSeq2) assembly using STAR.

Credits

The RAMPAGE data were produced by the Gingeras Lab at the Cold Spring Harbor Laboratory.

References

Batut PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21.