Execute Hi-C chromatin contact analysis pipelines

Execute ENCODE Hi-C pipeline from FASTQ to

Processing Hi-C FASTQ to 3D contact matrices and loop calls.

• · FASTQ files (paired-end or single-end)
• · Aligned BAM files

• · Quality control report
• · Contact/interaction matrix

• · Nextflow
• · Docker
• · BWA/Bowtie2 aligner
• · Juicer
• · HiCCUPS

• · Reference genome indexed
• · FASTQ files available
• · Nextflow/Docker installed

• · Poor FASTQ quality (low pass rate)
• · Reference genome mismatch
• · Memory exhaustion on large datasets
• · Adapter contamination

• · ENCODE consortium standards documented
• · Maintained in ammawla/encode-toolkit
• · Peer-reviewed publications cited
• · Citable references provided