BS-seq tracks Track Settings
 
BS-seq tracks

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BS-seq tracks

This is a BS-seq super track that groups together signal (bigWig format) regions (bigBed format). These tracks were produced by DANIO-CODE BS-seq pipeline that is adapted from the ENCODE pipeline. The pipeline consists of several steps, including quality trimming and filtering of raw reads, aligning reads to the C to T and G to A transformed and indexed genome respectively using Bismarck. The raw methylation data are showed in bigWig file obtained with coverage2cytosine tool, and extracted methylation are obtained with bismark_methylation_extractor tool which produce methylation report in CpG, CHG and CHH context. Quality metrics for each stage of the pipeline are included in the outputs. More about the pipeline can be found on this link: https://www.encodeproject.org/wgbs/.

Track definition: BS-seq tracks consist of 4 parts:

  1. BS-seq signal, showing the percentage of methylation of every C in the genome.
  2. CpG methylated regions, showing the methylation percentage of CpG regions.
  3. CHG methylated regions, showing the methylation percentage of CHG regions, with H is any base other than G.
  4. CHH methylated regions, showing the methylation percentage of CHH regions, with H is any base other than G.

Methylation status is shown with color codes: - red -> methylated - yellow -> 50% - green -> non-methylated

For more information on how the data were processed, please refer https://gitlab.com/da-bar/DANIO-CODE_BS-seq.