| 6 | 6 | * Call peaks (eg. MACS) or use another method to analyze enrichment and/or presumed binding. For ChIP-seq experiments profiling transcription factors (with discrete binding sites), binding site identification (via peak calling) is typically recommended. Peaks can be called without control; however, it's highly recommended to include a control sample (e.g. IgG or input, with input generally preferred over IgG). For ChIP-seq experiments profiling epigenetic (such as histone) modifications, however, modeling ChIP enrichment as peaks may not accurately describe the actual data, and some other (such as sliding window) quantification may be more relevant. |
