This repository contains tools and data related to Enzymatic Methylation Sequencing and Enzymatic 5hmC-seq (E5hmC-seq)
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 EM-seq paper)
Reference genomes containing spike-in methylation controls are available via an amazon s3 bucket: s3://neb-em-seq-sra/
- GRCh38: https://neb-em-seq-sra.s3.amazonaws.com/grch38_core%2Bbs_controls.fa
- T2T chm13 (hs1): https://neb-em-seq-sra.s3.amazonaws.com/T2T_chm13v2.0%2Bbs_controls.fa
To use the Nextflow v1 scripts in this repository you need an older version of nextflow.
NXF_VER=22.10.4 nextflow run em-seq.nf --genome em-seq_ref_files/T2T_chm13v2.0+bs_controls.fa --flowcell AAC27FDF --fastq_glob '*_R{1,2}.fastq*' -resume
We hope to upgrade to the NextFlow v2 syntax in the future.
You may also be interested in the nf-core methylseq project