The proto CpG island methylator phenotype of sessile serrated adenoma/polyps

Code and data analysis

This repository contains the code for the following paper:

• H Parker, S Orjuela, A Martinho Oliveira, F Cereatti, M Sauter, G Tanzi, A Weber, P Komminoth, S Vavricka, L Albanese, F Buffoli, MD Robinson and G Marra: The proto CpG island methylator phenotype of sessile serrated adenoma/polyps. Nov 2018. Epigenetics. paper

The structure of this repository is as follows:

• RNAseq/ Contains all the code in R and shell to obtain differentially expressed genes (DEGs) from bulk RNAseq data.

• RNAseq/STAR Contains the code to align fastq files using STAR, followed by the generation of bigwig and bedgraph files for visualization (for example in IGV). This is in a different folder, since these type of files cannot be generated with alignments generated by Salmon.

• RNAseq/Salmon> Contains the main pipeline to identify DEGs, using Salmon to align the fastq files. Pre-processing of data was done in shell, and further analysis in R.

• RNAseq/Data> Contains the DGEList object in an .RData file, as well as the metadata and the final list of differentially expressed genes for each comparison.

• BiSulf/ Contains all the code in R and shell to obtain differentially methylated sites (DMCs) and regions (DMRs) from targeted bisulfite sequencing data.

• BiSulf/Data Contains 6 lists: DMCs and DMRs identified in both Adenomas and SSA/Ps (4), list of annotated DMRs, and list of genes with their corresponding methylation and matched expression (for figure 4.D).