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

BMC Bioinformatics

Table 6 Duplicate level in three ER ChIP-Seq libraries

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

*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.
**Percentage over total duplicates in the library.

ISSN: 1471-2105