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:* /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:* /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