Peak calling allows the user to determine regions of the genome where target signal is significantly enriched in relation to background. This approach can be helpful to understand how a protein interacts with loci or other chromatin factors in a genome-wide analysis. CUTANATM Cloud offers peak calling with MACS2 and SICER2, which require the input of Unique BAM files generated by the CUTANATM Cloud Alignment pipeline.
Each peak caller tool has unique benefits depending on the enrichment pattern of the target; for narrowly enriched targets, MACS2 is recommended, for broadly enriched targets SICER2 is recommended. Either tool can be used for peak calling but it does help to know a priori how your target is expected to enrich so that an appropriate tool can be selected. Peak callers leverage significance thresholds for weighted comparisons of peaks. The output of peak calling for a single target is a BED file and text file that describe the genome location of each peak. The BED file can be loaded into IGV for visual confirmation of peak significance.