![]() The final PETs are used to generate a 2D contact-map file for visualization and also to identify clusters of overlapping intrachromosomal loops. The final tags (from all three categories of read pairs) are used to identify genomic binding sites of the protein of interest via peak calling. Haplotype-resolved chromatin interactions can be deduced if phased SNP information is available for the appropriate reference genome. ![]() Long-read ChIA-PET for base-pair resolution mapping of haplotype-specific chromatin interactions. ![]() The ChIA-PET pipeline (ChIA-PIPE) was developed by the Jackson lab. The full ChIA-PET pipeline code is available on Github.ĬhIA-PIPE is a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control assessment for each dataset. To enable visualization, ChIA-PIPE generates input files for two-dimensional contact map viewing with Juicebox and HiGlass and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. To enable structural interpretation, ChIA-PIPE calls chromatin contact domains, resolves allele-specific peaks and loops, and annotates enhancer-promoter loops. ![]() ChIA-PIPE also supports the analysis of other related chromatin-mapping data types. If multiple fastq files are generated, then fastq files are merged. Produced by trimming sequencing adaptors, identifying the ChIA-PET bridge linker sequence from input reads, collecting singlelinker 2 tags reads, mapping these filtered reads to the reference genome, quality filtering, deduplicating, and sorting. These reads are ChIA-PET single linker 2 tags, meaning two qualified genomic sequences connected with a linker, where both genomic sequences is larger than or equal to 18bp. ![]()
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