RNA-seq tracks Track Settings
 
RNA-seq tracks

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 Configure 		 27 Prim-5  DCD002238SQ  +  Prim-5, Busch-Nentwich_Lab, PRJEB12982   Data format 
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 Configure 		 27 Prim-5  DCD002238SQ  -  Prim-5, Busch-Nentwich_Lab, PRJEB12982   Data format 
    
Assembly: Zebrafish May 2017 (GRCz11/danRer11)

RNA-seq tracks

The whole RNA-seq dataset including raw data and metadata annotation can be found in the DANIO-CODE Data Coordination Center (https://danio-code.zfin.org/dataExport/?view=table&selected_facet=RNA-seq-assay_type)

This is a RNA-seq super track that groups together signal of RNA-seq data (bigWig format) of stranded and unstranded RNA-seq samples. regions (bigBed format).

The RNA-seq pipeline used to generate these tracks are described https://gitlab.com/danio-code/DANIO-CODE_RNA-seq.

Briefly, the pipeline consists of:
  1. Reference genome index generation (one time only).
  2. Alignment files with STAR: The part of the pipeline which maps the reads to the reference genome.
  3. Quality control of alignment: The second step which controls the quality of the alignments from STAR.
  4. bedGraph to bigWig signal conversion.

Track definition: RNA-seq tracks consist of 2 different types: #. RNA-seq signals for stranded samples, which consist of positive and negative strands. #. RNA-seq signals for stranded samples, which consist of collapsed positive strands.

For more information on how the data were processed, please refer https://gitlab.com/danio-code/ADANIO-CODE_RNA-seq.