Calculate average DNA methylation across regions of interest

[oneillkza]

Description

As a bioinformatician, I would like to calculate the average DNA methylation across a range of region types across the genome in a single cell, in order to create later overview plots of a given data set.

Estimate

5

Priority

MUST

Notes

@oneillkza has code which can be adapted for this

Regions should be able to be fed in via bed files; the best way to pass in a list of bed files in CWL should be investigated. Example region types: all gene bodies, all introns, all exons, all CpG islands, all promoters, all repetitive elements, known enhancer sites, etc.

One other thought: many of these may be contained within LOLA, and this is essentially the same task as #28 , in which case code could be replicated. It may be necessary to be able to take in a combination of LOLA data and external BED files, and we should think about how to combine these.

Actually, merging this with #28: As a bioinformatician, I would like to calculate the average DNA methylation across a series of known DNA-associated protein binding footprint regions based on ChIP-seq experiments, using data from the LOLA package (ie the ENCODE and Codex data sets), in order to later find binding footprints associated with DMRs/conditions.

ie: make one CWL tool that takes in BED files, and another that specifies LOLA data sets