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sartorlab / mint

A pipeline for the integration of DNA methylation and hydroxymethylation data
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Refactor visualization code to use annotatr #3

Closed rcavalcante closed 8 years ago

rcavalcante commented 8 years ago

Transition from the old bedtools + ggplot2 visualization code to pure annotatr. In addition to having "less moving parts", the annotations in annotatr are much better than what I threw together for the previous implementation.

rcavalcante commented 8 years ago

Will need to add something to process_bisulfite_align.sh to create a file for annotatr to read. Unfortunately, the methylKit / methylSig style input is not correct.

An alternative would be to add a different read function.

rcavalcante commented 8 years ago

Part of this refactoring will be to remove the annotations from mint.