A julia package for allele-specific methylation analysis.

JuliASM is based on the method in XXX, and it draws ideas from statistical physics and information theory to identify significant differences between the methylation patterns of each haplotype.

• julia v1.0.0 or greater.
• git.

JuliASM and dependencies can be installed via the following command:

julia -e 'using Pkg; Pkg.clone("[email protected]:jordiabante/JuliASM.jl.git")'

In a julia session run

pkg> test JuliASM

The package includes a small toy example for illustrative purposes. The example consists of two alleles a1 and a2. The former has a mean-methylation level of 0.9, while the later has 0.1. The mutual information is almost equal to 1 in all variants, and the permutation test returns p-values≈0. The output bedGraph files can be found in out_path. To run the toy example run the following commands in a julia session:

using JuliASM
dir = "/path/to/JuliASM.jl/test/"
bam1_path="$(dir)/bam/example.a1.bam"
bam2_path="$(dir)/bam/example.a2.bam"
fasta_path = "$(dir)/fasta/example.fa"
vcf_path = "$(dir)/vcf/example.vcf"
out_path="$(dir)/out/"
run_asm_analysis(bam1_path,bam2_path,vcf_path,fasta_path,out_path)

• Jordi Abante

This project is licensed under the MIT License - see the LICENSE.md file for details.

• Inspiration