Overview

  1. Methylation analysis of cf-DNA
    1. Downloads
    2. Requirements
    3. Required R packages
    4. R scripts
    5. Perl and shell scripts
    6. MetaData files
    7. AMF and MHL matrices
    8. Data files from simulation
  2. Methylation haplotype analysis version 1.2
    1. Downloads
    2. Requirements

    Methylation analysis of cf-DNA

    Updated: 2017-06-18
    Contact: Dinh Diep (hdinhdp@gmail.com)

    This software was developed for cf-DNA methylation analysis.

    Downloads

    Re-analysis Final Code and Data

    R code for reproducing Figure 2

    Software requirements

    1. Unix based environment with capability of running perl and shell scripts
    2. samtools version 1.2 or above must be installed
    3. R version 3.4 or above

    Required R packages

    -ggplot2
    -earth
    -skmeans
    -ModelMetrics
    -caret
    -ROCR
    -gplot2 (for heatmap)
    -reshape
    -compiler

    R scripts

    Perl and shell scripts

    Instructions: Please have the perl scripts in the working directory when running tumor_load_estimation.R. The shell and perl code package for making simulation file are provided to perform random sampling of sequencing reads and require both a list of fastq names (to be sampled) and a mapped BAM files (to pull the sampled reads from).

    MetaData files

    Instructions: These files provide descriptions of the samples.

    AMF and MHL matrices

    Instructions: These files are input data for R code above. AMF (average weighted methylation frequency) matrices are provided to perform analysis of AMF versus MHL.

    Data files from simulation

    Instructions: After downloading, use tar utility to uncompress all three data folders and have all the files in the working directory when running tumor_load_estimation.R

    Methylation haplotype analysis version 1.2

    Updated: 2017-05-31
    Contact: Dinh Diep (hdinhdp@gmail.com)

    This software was developed for methylation haplotype analysis.

    Downloads

    Methylation_Haplotype_Analysis_v1.2.tar.gz

    Requirements

    1. Unix based environment with capability of running perl and shell scripts
    2. samtools version 1.2 or above must be installed
    3. bedtools v2.26.0 or above must be installed

    No installation of this package is required.

    The following are modules included in this package for methylation haplotype analysis:


    analyzeMethylation - quantify methylation levels from haplotype files with one of AMF, IMF, and MHL.


    USAGE:   analyzeMethylation.sh [list of haplotype files] [region file] <MHL|AMF|IMF>


    MethylationHaplotypeGenerator_V1 - generate methylation haplotype files using version 1 code. Note that this version only works for data that have been aligned to hg19.

    USAGE:   MethylationHaplotypeGenerator_V1.sh <RRBS|WGBS> [target bed file] [cpg position file] [bam file] [output name prefix]


    MethylationHaplotypeGenerator_V2 - generate methylation haplotype files using version 2 code. This software is best used with BAM files generated from the BisReadMapper pipeline. Please make sure your BAM files contain flags for Crick reads in the reverse complementary orientation and that paired-end reads are matched by identical read IDs. Quality scores must be in PHRED 33 base.


    USAGE:   MethylationHaplotypeGenerator_V2.sh [cpg position file] [bam file] [output file prefix name]


    make_mappable_bins - generate mappable regions file from BAM


    USAGE:   ./scripts/make_mappable_bins.sh [merged bam file] [minimum mapping depth]


    getMHBs - generate methylation haplotype blocks using version 1 code. Make mappable bins first using the make_mappable_bins.sh shell script. Next, methylation haplotype block calling must be performed with MethylationHaplotypeGenerator scripts V1 or V2. V2 script can call a significantly greater number of haplotypes. In Guo et. al. 2017, we set a highly stringent PHRED score cut off using V1 which resulted in fewer methylation haplotypes. See information for methylation haplotype generator softwares. Version 1 of MethylationHaplotypeGenerator will require the mappable bin file above to be used as the target file. Methylation haplotype block identification can be performed with haplotype files generated from V1 or V2. Haploinfo file for chr22 from the 61 WGBS in Guo et. al. 2017 is provided to reproduce the MHBs for chr22.


    USAGE:   getMHBs.sh [haplotype file] [target bed] [minimum LD R2 cutoff] [output name prefix]