A tool allowing the flexible calculation of DNA methylation concordance and heterogeneity metrics in methyl-seq data.

conda config --add channels r
conda config --add channels bioconda
conda create -n methex python=3.8
conda activate methex
conda install -c bioconda pysam
pip3 install pandas

Each analysis is applied to a single sorted and indexed BAM file. If necessary, a BAM file can be sorted and indexed using samtools, e.g.

samtools sort sample_unsorted.bam -o sample.bam
samtools index sample.bam

All analyses require the reference genome sequence in an indexed FASTA file.

If necessary, a FASTA file can be indexed using samtools.

samtools faidx hg19.fa

See example.html for an example as well as instructions for how to make use of multiple processors for efficient genome-wide analyses.

Generating example output file example.html from example.qmd uses the jupyter Python package. It can be installed as follows.

pip3 install jupyter

The output can be generated using 'quarto'.

quarto render example.qmd