This repository contains a description of the bioinformatics methods associated to the manuscript.
Summary details about the analyses are given in the following files:
- DNA sequencing: alignment, variation and tumour purity
- Bisulfite sequencing: processing and alignment, methylation counting and 5mC/5hmC levels
- RNA sequencing: transcript alignment, quantification and levels
The scripts written during the development of the project are available in 20150501_methylation_brain/.
A bayesian approach to estimate 5mC/5hmC is available in 20160727_bayes_fisher_sim.
An exploration of the levels of 5mC/5hmC in gene bodies ia available in 20170425_genebody_5hmC.