Analyse methylation profiles¶

Identify genomic regions with and without methylation. The pipeline expects reads with the bisulfide conversion.

Purpose¶

Epigenetic marker for several diseases (e.g. oncology)
Compare between samples with different phenotype (e.g. tissues)

Required inputs¶

Sequenced reads in gzipped fastq format.
- each sample is represented by two gzipped fastq files
- standard output files of paired-end sequencing
Reference genome in fasta format

|-- reads/original
        |-- <sample_1>_R1.fastq.gz
        |-- <sample_1>_R2.fastq.gz
        |-- <sample_2>_R1.fastq.gz
        |-- <sample_2>_R2.fastq.gz
|-- reference/<reference>
        |-- <reference>.fa

Generated outputs¶

Summary report of methylation profiles in sequenced samples

Example¶

How to run example:

cd /usr/local/snakelines/example/mhv

snakemake \
   --snakefile ../../snakelines.snake \
   --configfile config_methylseq.yaml

Example configuration:

Planned improvements¶

Aggregate quality statistics of preprocess and mapping with the MultiQC
Include coverage tracks (Bismark can produce them as well)