Bismark Alignment

This step aligns bisulfite-treated sequencing reads to a reference genome.

bismark --genome <path_to_reference_genome> -1 <reads_R1.fq> -2 <reads_R2.fq> -o <output_directory>

• Key options:

  • --genome: Path to the reference genome directory preprocessed with bismark_genome_preparation.

  • -1 and -2: Specify paired-end reads. Use -U for single-end reads.

  • -o: Output directory for alignment files.

• Output:

  • Produces .bam alignment files.

  • Produces .report.txt and

  • unmapped_reads.fq.gz file.