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Tutorial.md

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Tutorial

Installation

Download from github

git clone https://github.com/PaoyangLab/MeH.git
cd MeH

Run example

Methylation heterogeneity profiling

The example data is in MeHdata folder.

input
  • Methylomes: bam file and bam.bai
  • Reference genome: fa and fai
python MeHscr.py -w 4 -c 4 --CG
output
  • MeHscreening.log
  • /MeHdata/sample.0.csv files for each sample
    • CG_AT31test_0.csv
    • CG_AT33test_0.csv
    • CG_AT35test_0.csv
    • CG_AT37test_0.csv
  • /MeHdata/CG_Results.csv files for summary results

Subsequent analysis

Transform Results.csv to .bedGraph for IGV visualisation

input
  • MeHdata/CG_Results.csv files
Rscript tobed.R -m ./MeHdata/CG_Results.csv
output
  • Meh_result.bedGraph
    • PW_AT31test.bedGraph
    • PW_AT33test.bedGraph
    • PW_AT35test.bedGraph
    • PW_AT37test.bedGraph

finding DHR

input
  • MeHdata/CG_Results.csv files
  • genelist.txt for match the gene
Rscript finddhr.R -m ./MeHdata/CG_Results_test.csv -g ./MeHdata/genelist.txt -o ./MeHdata/CG -s W,W,D,D -p 1000
output
  • CG_DHR_Result.csv shows the list of DHR in down/up regulated genes/promoters
  • CG_MeH_Result.csv shows the table with the differnece of MeH regions