CAGE-seq tracks Track Settings
CAGE-seq tracks

Maximum display mode:       Reset to defaults   
Select views (Help):
regions       signal ▾      
Select subtracks by developmental stage:
  Developmental stage 1-cell  64-cell  512-cell  High  Oblong  Sphere  30%-epiboly  Shield  14-19 somites  Prim-5  Prim-25  90 Days-2 Years Developmental stage  
Select subtracks further by: (select multiple categories and items - help)
Track kind:
Sequencing sample:
Enumerated stage:

List subtracks: only selected/visible    all    ()
  Enumerated stage↓1 Sequencing sample↓2 Track kind↑3   Track Name↓4  
 27 Prim-5  DCD001532SQ  signal  Prim-5, Mueller_lab, SRA055273   Schema 

CAGE-seq tracks

The whole CAGE-seq dataset including raw data and metadata annotation can be found in the DANIO-CODE Data Coordination Center (

This is a CAGE-seq super track that groups together signal (bigWig format) and tag cluster regions (bigBed format). These tracks were produced by the DANIO-CODE CAGE-seq pipeline.

The main processing pipeline of the DCC ("CAGE_pipeline_v1.6") consists of 4 different processing steps :
#.Sequence quality filtering / trimming (FastQC) #.Mapping to the reference genome (Bowtie) #.Tag clustering (Paraclu-9)

There is also an additional signal conversion step for reformatting the input from the main pipeline to adequate UCSC track input format (DANIO-CODE CAGE-seq signal conversion pipeline v1.0).

Track definition: CAGE-seq tracks consist of 2 parts: #. CAGE-seq TSS signals #. and CAGE-seq tag clusters

For more information on how the data were processed, please refer