peiyulin/methylc repository overview

⁠Docker for MethylC-analyzer

⁠Installation

pull the official docker image by running:

docker pull peiyulin/methylc

⁠Usages

To use the MethylC-Analyzer Docker container, the folder has to be mounted from the host system into the container with the -v argument. The examples mount the current working directory under /app inside the container and then run the command:

docker run --rm -v $(pwd):/app peiyulin/methylc:V1.0 python /MethylC-analyzer/scripts/MethylC.py -h

usage: MethylC.py [-h] [-a GROUP1] [-b GROUP2] [-d DEPTH] [-r REGION]
                  [-q QUALIFIED] [-context CONTEXT] [-hc HEATMAP_CUTOFF]
                  [-dmrc DMR_CUTOFF] [-test TESTMETHOD] [-pvalue PVALUE]
                  [-bs BIN_SIZE] [-p PROMOTER_SIZE]
                  command samples_list input_gtf_file path_to_files

for example:

cd path_to_data/

docker run --rm -v $(pwd):/app peiyulin/methylc:0.1:latest python /MethylC-analyzer/scripts/MethylC.py command /app/input /app/output /app/ 

⁠Examples

Download the demo input files:

wget --no-check-certificate https://paoyang.ipmb.sinica.edu.tw/MethylC-analyzer/Demo.tar.gz
tar -xvf Demo.tar.gz
cd Demo

⁠Run it all in one

Run all the functions in MethylC-analyzer in one command by using all:

docker run --rm -v $(pwd):/app peiyulin/methylc:V1.0 python /MethylC-analyzer/scripts/MethylC.py all samples_list.txt TAR10_2_demo.gtf /app/ -a MT -b WT -d 4 -r 200 -q 2 -bs 200000 -pvalue 0.1

Input

• Samples CGmap files

• A GTF file

• A sample list txt file for sample description

  • The file is tab-delimited without a header

    ### samples_list.txt in Demo
    MT1     MT1s.CGmap.gz   MT
    MT2     MT2s.CGmap.gz   MT
    WT1     WT1s.CGmap.gz   WT
    WT2     WT2s.CGmap.gz   WT
    

    Copy

    Format descriptions:

    (1) sample_name (2) CGmap_location (3) group

⁠Run it separately

⁠Heatmap & PCA Analysis

docker run --rm -v $(pwd):/app peiyulin/methylc:V1.0 python /MethylC-analyzer/scripts/MethylC.py Heatmap_PCA samples_list.txt TAR10_2_demo.gtf /app/ -a MT -b WT -d 4 -r 200 -q 2 -bs 200000 -pvalue 0.1

Output

• Text files

  • Common region of each context: CommonRegion_CG.txt, CommonRegion_CHG.txt, CommonRegion_CHH.txt

  • Methylation union site: Unionsite.txt

  • Log of plotting: plot.log

• Bed files

  • Merge bed files: gtf_introns_merge.bed, gtf_3utr_merge.bed, gtf_5utr_merge.bed, gtf_Promoter_merge.bed, gtf_exons_merge.bed, gtf_cds_merge.bed, gtf_Genebody_merge.bed

  • bed6 files: gtf_Promoter_bed6.bed, gtf_Genebody_bed6.bed, .gtf_IGR_bed6.bed

• Figures

  • Heatmap: Heatmap_CG_0.2.pd

  • PCA: PCA_CG_0.2.pdf

  • The average methylation for each context: Average_methylation_levels.pdf

⁠Identify DMR

docker run --rm -v $(pwd):/app peiyulin/methylc:V1.0 python /MethylC-analyzer/scripts/MethylC.py DMR samples_list.txt TAR10_2_demo.gtf /app/ -a MT -b WT -d 4 -r 200 -q 2 -bs 200000 -pvalue 0.1

Output

• Text files
  • DMR for CG context: DMR_CG_all_0.1.txt, DMR_CG_hyper_0.1.txt, DMR_CG_hypo_0.1.txt

⁠Identify DMG

docker run --rm -v $(pwd):/app peiyulin/methylc:V1.0 python /MethylC-analyzer/scripts/MethylC.py DMG samples_list.txt TAR10_2_demo.gtf /app/ -a MT -b WT -d 4 -r 200 -q 2 -bs 200000 -pvalue 0.1

Output

• Text files

  • Hyper DMG list: DMG_CG_hyper_0.1_Genebody_list.txt, DMG_CG_hyper_0.1_Promoter_list.txt

  • Hypo DMG list: DMG_CG_hypo_0.1_Genebody_list.txt, DMG_CG_hypo_0.1_Promoter_list.txt

• Bed files

  • bed for DMR: DMR_CG_all_0.1.txt.bed, DMR_CG_hypo_0.1.txt.bed, DMR_CG_hyper_0.1.txt.bed

• Figure

  • Bar chart for DMG: Summary_DMR_DMG_numbers_CG_0.1.pdf

⁠Fold Enrichment Analysis

docker run --rm -v $(pwd):/app peiyulin/methylc:V1.0 python /MethylC-analyzer/scripts/MethylC.py Fold_Enrichment samples_list.txt TAR10_2_demo.gtf /app/ -a MT -b WT -d 4 -r 200 -q 2 -bs 200000 -pvalue 0.1

• Bed files

  • for common regions: CommonRegion_CG.txt.bed
  • bed.bed files

• Figures

  • Fold_Enrichment plot: CG_Fold_Enrichment.pdf

⁠Chromosome View Analysis

docker run --rm -v $(pwd):/app peiyulin/methylc:V1.0 python /MethylC-analyzer/scripts/MethylC.py ChrView samples_list.txt TAR10_2_demo.gtf /app/ -a MT -b WT -d 4 -r 200 -q 2 -bs 200000 -pvalue 0.1

Output

• Text files

  • Chromosome view of each sample: MT1_200000_chrView.txt, MT2_200000_chrView.txt, WT1_200000_chrView.txt, WT2_200000_chrView.txt
  • Chromosome view list: chrView_delta_list.txt, chrView_delta.txt, chrView_list.txt

• Figures

  • Chromosome view of each context: chrView_CG.pdf, chrView_CHG.pdf, chrView_CHH.pdf
  • Delta chromosome view of each context: chrView_delta_CG.pdf, chrView_delta_CHG.pdf, chrView_delta_CHH.pdf

⁠Metaplot Analysis

docker run --rm -v $(pwd):/app peiyulin/methylc:V1.0 python /MethylC-analyzer/scripts/MethylC.py Metaplot samples_list.txt TAR10_2_demo.gtf /app/ -a MT -b WT -d 4 -r 200 -q 2 -bs 200000 -pvalue 0.1

Output

• text files

  • metaplot_delta_CG.txt, metaplot_delta_CHG.txt, metaplot_delta_CHH.txt

• bigwig files

  • For each sample and each context: MT1_CG.bw, MT1_CHG.bw, MT1_CHH.bw, MT2_CG.bw, MT2_CHG.bw, MT2_CHH.bw, WT1_CG.bw, WT1_CHG.bw, WT1_CHH.bw, WT2_CG.bw, WT2_CHG.bw, WT2_CHH.bw

• Matrix

  • MT1_CHH.matrix.gz, MT2_CHH.matrix.gz, MT2_CHH.matrix.gz, MT2_CHH.matrix.gz,

• Figures

  • Meta gene plots for each context: metaplot_CG.pdf, metaplot_CHG.pdf, metaplot_CHH.pdf
  • Meta gene plots for each context: metaplot_delta_CG.pdf, metaplot_delta_CHG.pdf, metaplot_delta_CHH.pdf