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