For each ChIA-PET library, we first perform a QA test sequencing to generate 5 million to 10 million PET reads from a MiSeq run, which can usually test two to four ChIA-PET libraries. Once a quality library is verified by the test sequencing data, we then generate ~200 million PET reads from a HiSeq “production” run. The test and production sequencing data are both processed using ChIA-PIPE, detailed below. Now, the pipeline provides library-level quality examination, i.e., sequencing alignment quality, peak intensity tornado plot [generated by deepTools2 (30)], loop spanning distribution, and loop-level anchor support distribution. The contact map file generated by the pipeline is ready to be examined by Juicebox (.hic) or HiGlass (.cool).

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