Summary

methclone can efficiently analyzes genome-wide DNA methylation data to identify the epigenetic loci that harbor large changes in the clonality of the epigenetic alleles (epialleles). We quantify the changes using a composition entropy calculation (ΔS) and also introduce a new measure of global clonality shift, epialleles per million CpGs (EPM), which enables comparisons between different samples to gauge global changes in epiallelic diversity.

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Download

Click on "Source", "Browse", and then "Download zip"

Installation

unzip methclone.zip cd /path/to/methclone/src/utils/BamTools/ make cd /path/to/methclone/src/utils/gzstream/ make cd /path/to/methclone/src/ make

Usage

./methclone stage1.bam stage2.bam output.txt.gz sampleID

Example

cd /path/to/methclone/ ./bin/methclone example/chr22-1.bam example/chr22-2.bam chr22.output.txt.gz chr22-1-2

Output

The output file of methclone is a text file with 46 columns. First 14 columns are described as below:

| column name | description | |:------------|:------------| | chr | chrosomome | | start | start position | | end | end position | | sample | sample names in the comparison | | distance | length of the genomic locus | | strand | strand information | | loci | the four position of the CpGs in the genomic locus | | entropy | the delta entropy to evaluate the epialellele shift. The low the delta entropy, the higher the epiallele shift | | read1 | number of reads covered this genomic locus in the first sample | | read2 | number of reads covered this genomic locus in the second sample | | meth1 | the average methylation levels of this genomic locus in the first sample | | meth2 | the average methylation levels of this genomic locus in the second sample | | pattern1 | the dominant methylation patterns of this genomic locus in the first sample | | pattern2 | the dominant methylation patterns of this genomic locus in the second sample |

15th to 31st columns is the percentage of reads support each of the 16 patterns of DNA methylation at this genomic locus in the first sample.

32nd to 46th columns is the percentage of reads support each of the 16 patterns of DNA methylation at this genomic locus in the second sample.