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Reference Assembly
GCA_900231805.1Paired-End Sequencing Data
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CUT&RUN/CUT&TAG Analysis: Protein-DNA Interaction Mapping
Description
Complete CUT&RUN/CUT&TAG analysis workflow for paired-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt) and alignment (Bowtie2 with dovetail option enabled). Applies quality filtering (MAPQ ≥ 30, concordant pairs only), converts BAM to BED format, and performs peak calling using MACS2 with parameters optimized for the punctate signal profile characteristic of CUT&RUN/CUT&TAG experiments.