Download, pick, and generate data of specific genomic contexts.

[yuzhong-deng]

To pick the interested region of specific genomic contexts and generate datasets for them, an example of GRCm39/mm39 on chromosome [10] is performed (Original build in the paper is Ensembl build 104).

There are three types of raw files:

• Regulatory Features: promoter, enhancers, TFBS, open chromatin, CTCF BS
• Featuer types: Exons, CDS
• Histone binding sites: H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9ac, H3K9me3, p300
• CpG featuers: CpG islands, CpG shores

Two main steps are included respectively:

• Download
• Pick interested regions and generate the corresponding dataset
  • Pick interested regions and corresponding index
  • Generate dataset by new index

[gdewael]

Much appreciated!