FASTQ-to-peaks ChIP-seq pipeline: Bowtie2 align, Picard dedup, MACS2/MACS3 narrow/broad peak calling, FRiP/IDR QC, deepTools bamCoverage/heatmaps. Use for ChIP-seq/CUT&RUN peak calling or FRiP/NRF/IDR QC.
FASTQ-to-peaks ChIP-seq pipeline: Bowtie2 align, Picard dedup, MACS2/MACS3 narrow/broad peak calling, FRiP/IDR QC, deepTools bamCoverage/heatmaps. Use for ChIP-seq/CUT&RUN peak calling or FRiP/NRF/IDR QC.
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