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

Display mode:       Reset to defaults   

Display read names
Attempt to join paired end reads by name
Minimum alignment quality:

Color track by bases: Help on base coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion

Additional coloring modes:
Color by strand (blue for +, red for -)
Use gray for
Use R,G,B colors specified in user-defined tag
No additional coloring

Display data as a density graph:

BAM configuration help

Select subtracks by replicate and stage: (help)
 All Replicate Replicate 1  Replicate 2 
Stage
Adult Female 
Embryo 
List subtracks: only selected/visible    all  
 
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 Configure 		 Adult Females Replicate 1  RAMPAGE Alignments for Replicate 1 of Adult Females Sample   Schema 
 
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 Configure 		 Adult Females Replicate 2  RAMPAGE Alignments for Replicate 2 of Adult Females Sample   Schema 
 
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 Configure 		 Embryos Replicate 1  RAMPAGE Alignments for Replicate 1 of Embryos Sample   Schema 
 
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 Configure 		 Embryos Replicate 2  RAMPAGE Alignments for Replicate 2 of Embryos Sample   Schema 

Description

These tracks show the alignment 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.