Figure 4. ChIP-Sequencing Analysis.

Analysis of sequencing reads from ChIP involves quality control, mapping, and peak calling. Low quality reads and bases (dashed lines) are removed from analysis to improve alignment. Remaining reads are aligned to the genome. Reads are extended to the fragmentation size obtained in sonication to more precisely map binding sites (arrows). Enrichment scores and permutations are used to obtain statistical significance for enriched genomic regions.