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