The CHIPs pipeline is designed to perform robust quality control and reproducible processing of the chromatin profile sequencing data derived from ChIP-seq, DNase-seq, and ATAC-seq. CHIPs analysis is implemented across ten main procedures: Read alignment; Quality control; Sample contamination; Copy number variation calling; Peak calling; Fraction of reads in peaks (FRIP) score and PCR bottleneck coefficient (PBC); Annotation with the cis-regulatory element annotation system (CEAS), including intersection with union DNase I hypersensitive sites (DHS); Gene target prediction; Motif enrichment; Evolutionary conservation. The inputs to the pipeline are FASTQ/BAM format DNA sequence read files. The pipeline itself is encoded in the workflow language snakemake and executed in a conda environment using the cluster engine. The workflow is shown here. For any questions contact the developers at



The details of other software used in CHIPs are written to software_versions_all.txt in the directory where this report was generated.

Name Version Build Channel
0 bedtools 2.27.1 he513fc3_4 bioconda
1 bwa 0.7.15 1 bioconda
2 fastp 0.20.1 h8b12597_0 bioconda
3 fastqc 0.11.9 0 bioconda
4 homer 4.11 pl526hc9558a2_3 bioconda
5 macs2 py36h4c5857e_1 bioconda
6 pybedtools 0.8.1 py36h5202f60_2 bioconda