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ATAC-seq Analysis: Chromatin Accessibility Profiling

Complete ATAC-seq analysis pipeline for paired-end reads. Processes raw FASTQ data through adapter and bad quality removal (cutadapt), alignment (Bowtie2 end-to-end), and filtering (removes MT reads, discordant pairs, low mapping quality <30, PCR duplicates). Generates 5' cut site pileups (±100bp), performs peak calling, and quantifies reads in 1kb summit-centered regions. Produces two normalized coverage tracks (per million mapped reads and per million reads in peaks) and fragment length distribution plots for quality assessment.

C57BL/6J