How is ChIP-Seq data analyzed to identify transcription factor binding sites?

ChIP-Seq analysis identifies DNA regions bound by proteins. Pipeline: 1) Quality control and preprocessing - FastQC, adapter trimming, filter low-quality reads. 2) Alignment - map reads to reference genome using Bowtie2 or BWA (allow multi-mappers carefully). 3) Peak calling - identify enriched regions using MACS2, which models fragment size and compares to input/IgG control. Broad peaks for histone modifications, narrow for transcription factors. 4) Peak annotation - assign peaks to nearby genes using ChIPseeker or HOMER, analyze genomic distribution. 5) Motif discovery - identify enriched sequence motifs using HOMER, MEME-ChIP. 6) Differential binding analysis - DiffBind compares binding between conditions. Integrative analysis with RNA-Seq reveals regulatory networks.