Skip to main content

Table 6 Duplicate level in three ER ChIP-Seq libraries

From: HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

Library Type* Size (Mb) Non-duplicates (M) Duplicates (M) Sum (M) Duplicates (%) Portion (%)**
IP_1 All peaks 17.08 4.34 3.24 7.58 42.73 60.23
IP_1 Top peaks 3.33 1.92 2.54 4.46 57.03 47.3
IP_1 Non-peak 3049.89 12.27 2.08 14.35 14.51 38.71
IP_1 Total 3080.44 16.9 5.38 22.27 24.13 100
IP_2 All peaks 12.54 2.94 1.1 4.04 27.3 69.79
IP_2 Top peaks 2.31 1.2 0.9 2.11 42.84 57.12
IP_2 Non-peak 3058.77 17.9 0.47 18.36 2.54 29.55
IP_2 Total 3080.44 21.08 1.58 22.66 6.98 100
IP_3 All peaks 15.94 4.87 2.69 7.56 35.53 70.87
IP_3 Top peaks 3.02 1.97 2.05 4.02 51.04 54.1
IP_3 Non-peak 3053.24 20.11 1.08 21.19 5.09 28.46
IP_3 Total 3080.44 25.36 3.79 29.15 13.01 100
  1. *The non-peak regions are these after excluding regions from −100 bp to +100 bp of all peaks; the top peaks refer to the top 10% of the peaks with the smallest p values.
  2. **Percentage over total duplicates in the library.