Prim-5, Busch-Nentwich_Lab, PRJEB12982 (hub_280355_DCD002168SQ_pos)
  Position: chr10:33,840,892-34,129,251
Total Bases in view: 288,360
Statistics on: 708 items covering 12,530 bases (4.35% coverage)
Average item spans 17.70 bases. Minimum span 1 maximum span 100
Average value 0.454411 min 0.10439 max 1.46143 standard deviation 0.308319
View table schema

Go to RNA-seq tracks track controls

Data last updated at UCSC: 2018-05-25 15:50:06

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.