6 Coverage Analysis

Read coverage is an important factor for interpreting DNA methylomes.

It requires different coverage levels for different purpose. For example, SNV calling requires higher coverage than it is required for DMR study. The SNV calling process is depending on all nucleotides (A, T, C and G), whereas DNA methylation levels only depend on T and C read counts aligned to cytosines.

In CGmapTools, we propsed two ways for evaluating the coverages of DNA methylations: OverAll Coverage (OAC) and Methylation-Effective Coverage (MEC).

  • OAC is calculated as the average read coverage on all nucleotides on both strands, which are calculated from the ATCGmap file.
  • MEC is calculated as the average read coverage only for cytosines, which is calculated from the CGmap file. Generally, the MEC is slightly higher than half of the OAC.

In CGmapTools, we provides function for basic statistics of coverages (cgmaptools oac stat and cgmaptools mec stat) and visualization of coverages in bins across genome (cgmaptools oac bin and cgmaptools mec stat).

6.1 oac

  • Command
cgmaptools oac -h
#   Usage:    cgmaptools oac <command> [options]
#   Version:  0.1.2
#   Updated on: Dec. 14th, 2018
#   Commands:
#        bin      * overall coverage in bins
#        stat     * overall coverage statistics globally

6.1.1 oac bin

  • Command
cgmaptools oac bin -h
#   Usage: cgmaptools oac bin  [-i <ATCGmap>] [-B 5000000] 
#          (aka ATCGmapCovInBins)
#   Description: Generate the overall coverage in Bins.
#   Contact:     Guo, Weilong; guoweilong@126.com;
#   Last Update: 2016-12-07
#   Output Ex:
#      chr1    1       5000    29.0000
#      chr1    5001    10000   30.0396
#      chr2    1       5000    35.0755
#      chr2    5001    10000   40.0027
#      chr3    1       5000    na
#   
#   Options:
#     -h, --help            show this help message and exit
#     -i FILE               File name end with .ATCGmap or .ATCGmap.gz. If not
#                           specified, STDIN will be used.
#     -B BIN_SIZE           Define the size of bins [Default: 5000000]
#     -f FILE, --figure-type=FILE
#                           png, pdf, eps. Will not generate figure if not
#                           specified
#     -H FLOAT              Height of figure in inch [Default: 4]
#     -W FLOAT              Width of figure in inch [Default: 8]
#     -p STRING             Prefix for output figures
#     -t STRING, --title=STRING
#                           title in the output figures

  • Example

    cgmaptools oac bin -i WG.ATCGmap.gz -B 1000 -f png -p WG -t WG > WG.oac_bin.data

  • Output figure

MEC example

Figure 6.1: MEC example

6.1.2 oac stat

  • Command
cgmaptools oac stat -h
#   Usage: cgmaptools oac stat [-i <ATCGmap>]
#          (aka ATCGmapStatCov)
#   Description: Get the distribution of overall coverages.
#   Contact:     Guo, Weilong; guoweilong@126.com;
#   Last Update: 2018-05-02
#   Output Ex:
#      OverAllCov      global  47.0395
#      OverAllCov      chr1    45.3157
#      OverAllCov      chr10   47.7380
#      CovAndCount     1       1567
#      CovAndCount     2       655
#      CovAndCount     3       380
#   
#   Options:
#     -h, --help            show this help message and exit
#     -i FILE               File name end with .ATCGmap or .ATCGmap.gz. If not
#                           specified, STDIN will be used.
#     -f FILE, --figure-type=FILE
#                           png, pdf, eps. Will not generate figure if not
#                           specified
#     -H FLOAT              Scale ratio for the Height of figure [Default: 4]
#     -W FLOAT              Width of figure in inch [Default: 8]
#     -p STRING             Prefix for output figures

  • Example

    cgmaptools oac stat -i WG.ATCGmap.gz -p WG -f png > WG.oac_stat.data

  • output format:

    The output format of bin:

    chr1    1       5000    29.0000
chr1    5001    10000   30.0396
chr2    1       5000    35.0755
chr2    5001    10000   40.0027
chr3    1       5000    na

    The output format of stat:

    OverAllCov      global  47.0395
OverAllCov      chr1    45.3157
OverAllCov      chr10   47.7380
CovAndCount     1       1567
CovAndCount     2       655
CovAndCount     3       380

6.2 mec

  • Command
cgmaptools mec -h
#   Usage:    cgmaptools mec <command> [options]
#   Version:  0.1.2
#   Updated on: Dec. 14th, 2018
#   Commands:
#        bin      * methylation effective coverage in bins
#        stat     * methylation effective coverage statistics globally

6.2.1 mec bin

  • Command
cgmaptools mec bin -h
#   Usage: cgmaptools mec bin [-i <CGmap>] [-B 5000000] 
#         (aka CGmapCovInBins)
#   Description: Generate the methylation-effective coverage in Bins.
#   Contact:     Guo, Weilong; guoweilong@126.com;
#   Last Update: 2018-01-02
#   Output Ex:
#      chr1    1       5000    29.0000
#      chr1    5001    10000   30.0396
#      chr2    1       5000    35.0755
#      chr2    5001    10000   40.0027
#      chr3    1       5000    na
#   
#   Options:
#     -h, --help            show this help message and exit
#     -i FILE               File name end with .CGmap or .CGmap.gz. If not
#                           specified, STDIN will be used.
#     -B BIN_SIZE           Define the size of bins [Default: 5000000]
#     -f FILE, --figure-type=FILE
#                           png, pdf, eps. Will not generate figure if not
#                           specified
#     -H FLOAT              Height of figure in inch [Default: 4]
#     -W FLOAT              Width of figure in inch [Default: 8]
#     -p STRING             Prefix for output figures
#     -t STRING, --title=STRING
#                           title in the output figures
#     -C CONTEXT, --context=CONTEXT
#                           specific context: CG, CH, CHG, CHH, CA, CC, CT, CW
#                           use all sites if not specified

  • Example

    cgmaptools mec bin -i WG.CGmap.gz -B 1000 -f png -p WG -t WG > WG.mec_bin.data

6.2.2 mec stat

  • Command
cgmaptools mec stat -h
#   Usage: cgmaptools mec stat [-i <CGmap>]  
#         (aka CGmapStatCov)
#   Description: Get the distribution of methylation-effective coverages.
#   Contact:     Guo, Weilong; guoweilong@126.com
#   Last Update: 2018-05-02
#   Output Ex:
#      MethEffectCove  global  47.0395
#      MethEffectCove  chr1    45.3157
#      MethEffectCove  chr10   47.7380
#      CovAndCount     1       1567
#      CovAndCount     2       655
#      CovAndCount     3       380
#   
#   Options:
#     -h, --help            show this help message and exit
#     -i FILE               File name end with .CGmap or .CGmap.gz. If not
#                           specified, STDIN will be used.
#     -f FILE, --figure-type=FILE
#                           png, pdf, eps. Will not generate figure if not
#                           specified
#     -H FLOAT              Scale factor for the Height of figure [Default: 4]
#     -W FLOAT              Width of figure in inch [Default: 11]
#     -p STRING             Prefix for output figures
#     -C CONTEXT, --context=CONTEXT
#                           specific context: CG, CH, CHG, CHH, CA, CC, CT, CW
#                           use all sites if not specified

  • Example

    cgmaptools mec stat -i WG.CGmap.gz -p WG -f png > WG.mec_stat.data

  • Output figure

MEC example

Figure 6.2: MEC example