Bismark - Methylation Extractor

Reads in a bisulfite read alignment results file produced by the Bismark bisulfite mapper and extracts the methylation information for individual cytosines

Location

  • Filepath: <SnakeLines_dir>/rules/shared/mapping/report/methylation/bismark.snake
  • Rule name: bismark__methylation_extractor

Input(s):

  • bam: mapped reads with Bismark in BAM format
  • ct_index: CT reference index (created by rule bismark__prepare_index)
  • ga_index: GA reference index (created by rule bismark__prepare_index)
  • ref: reference genome, i.e. reference/{reference}/{reference}.fa

Output(s):

  • mbias_report: report generated by the bismark_methylation_extractor tool
  • splitting_report: report generated by the bismark_methylation_extractor tool

Bismark - Summary Report

Aggregate results from several methylation statistic files generated by Bismark into single summary HTML report

Location

  • Filepath: <SnakeLines_dir>/rules/shared/mapping/report/methylation/bismark.snake
  • Rule name: bismark__summary_report

Input(s):

  • alignment_report: Report generated with Bismark together with read alignment
  • splitting_report: Report generated by the bismark_methylation_extractor tool
  • mbias_report: Report generated by the bismark_methylation_extractor tool

Output(s):

  • html: Aggregated quality report of discovered methylation