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SelectMethContext

Separate cytosines based on the methylation context in which they occur and produces statistics about context methylation.

Version 1.0
Bundle sequencing
Categories Alignment
Authors Chiara Facciotto (chiara.facciotto@helsinki.fi)
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Source files component.xml SelectMethContext.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
methCall CSV Mandatory File containing the methylation percentages obtained from after the methylation calling (MethCalling function), containing a column wth the context at which methylation occurs (i.e., either CpG, CHG or CHH, where H can be A, T or C).

Outputs

Name Type Description
cpg CSV CSV file containing all cytosines (methylated or not) at CpG context.
chg CSV CSV file containing all cytosines (methylated or not) at CpG context.
chh CSV CSV file containing all cytosines (methylated or not) at CpG context.
statistics CSV CSV file containing the percentage of methylation occuring at CpG, CHG and CHH context. In this case only the methylated cytosines are considered in the analysis.

Parameters

Name Type Default Description
coverage int 10 Minimum read coverage a cytosine needs to have in order for its methylation percentage to be considered reliable. If the coverage is under this threshold the cytosine will still appear in the the context file but it will not be used to compute the statistics.
methPerc float 0.5 Minimum methylation percentage a cytosine needs to have in order to be considered methylated. If the methylation percentage is under this threshold the cytosine will still appear in the the context file but it will not be used to compute the statistics. The percentage is represented by values between 0 and 1.

Test cases

Test case Parameters IN
methCall
OUT
cpg
OUT
chg
OUT
chh
OUT
statistics
case1_default (missing) methCall cpg chg chh statistics
case2_coverage properties methCall cpg chg chh statistics

# Testing SelectMethContext component,
coverage=4

case3_methPerc properties methCall cpg chg chh statistics

# Testing SelectMethContext component,
methPerc=0.7


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