This repository contains tools and data related to Enzymatic Methylation Sequencing.

There are 3 nextflow scripts:

• em-seq.nf (to align reads, filter and call methylation)
• bins.nf (to calculate binned coverage around the TSS
• cov_vs_meth.nf (to generate the "coverage by feature type" figure from the paper)

A GRCh38 reference genome containing spike-in methylation controls is available via an amazon s3 bucket: s3://neb-em-seq-sra/grch38_core+bs_controls.fa or via https: https://neb-em-seq-sra.s3.amazonaws.com/grch38_core%2Bbs_controls.fa

See https://www.biorxiv.org/content/10.1101/2019.12.20.884692v2 for method details and use of these tools.