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. Author manuscript; available in PMC: 2020 Apr 15.
Published in final edited form as: Nat Protoc. 2019 Nov 13;14(12):3275–3302. doi: 10.1038/s41596-019-0218-7

Figure 2 |. ICeChIP-seq Bioinformatics Analysis Pipeline.

Figure 2 |

Workflow for analysis of ICeChIP-seq data. IP and Input FastQ paired-end reads are mapped and filtered for quality and mononucleosomal size into their respective alignment Bed files. From these Bed files, genome-wide coverage BedGraph files are generated and merged to compute the fold change of the IP over Input at genomic loci as a BedGraph file. This ratiometric BedGraph file is then calibrated to the nucleosome standard enrichment to generate the final HMD BedGraph file.