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:
BS-seq tracks consist of 4 parts:
- BS-seq signal, showing the percentage of methylation of every C in the genome.
- CpG methylated regions, showing the methylation percentage of CpG regions.
- CHG methylated regions, showing the methylation percentage of CHG regions, with H is any base other than G.
- 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.