Bismark Deduplication

This step removes duplicate reads to avoid overestimating methylation levels.

deduplicate_bismark ${paired_end} $args --bam $bam

• Key options:

  • args options use all arguments from bismark deduplicate command.

  • --paired: Use this for paired-end data. Remove for single-end reads.

  • --bam: Specifies the input BAM file, generated from bismark alignment

• Output:

  • Generates a deduplicated .bam file.

  • Produces deduplicated_report.txt file.