hichipper QC report

Summary Tables

	K562_Rep1	K562_Rep3	K562_Rep2
Total PETs	213165389	178162951	155907950
% Reads in Anchors	56.47	57.56	71.59
% HQ Unique Mapped	106.67	100.20	106.81
% Long Range Interaction	21.55	18.17	22.78
% in Loops	1.65	1.53	2.27

The first summary table notes how many PETs are in each sample and what fraction were mapped with high-quality. First, the “% Reads in Anchors” takes all unique, mappable pairs (whether they are valid, dangling, self-circle, etc. doesn’t matter) and determines what fraction have both overlapping with anchor loci. Note, this numer should give an indication of the ChIP quality, but it may be sensitive to how peaks are determined with padding, etc. While the “% HQ Unique Mapped” reads should be self explanatory, the “% Long Range Interaction” value represents the number of intrachromosomal reads longer than the minimum length (default 5Kb) specified by the user and is a good approximation for the efficacy of the in situ ligation. Finally, the “% in Loops” is the fraction of total reads that are in loops, defined by high-quality, mapped intrachromosomal, anchor-mapped, between min and max lengths (default 5Kb and 2Mb). If the proportion of loops reads is low but the proportion of long range interactions is high, this suggests that the ChIP efficiency is relatively low.

	K562_Rep1	K562_Rep3	K562_Rep2
Intrachromasomal PETs	73198912	52708198	55118481
% Reads < 5Kb	25.07	27.85	25.05
% Reads in 5KB-2Mb	62.76	61.41	64.44
% Reads > 2Mb	12.17	10.74	10.51

The second summary table shows the total number of intrachromosomal pets and the distance that they span binned by the max and min user defined distances. Only reads in the middle are used when making loops but all are used for anchor calling. If the very long interactions are disproportionately abundant, the proximity ligation step may not have been effective. In contrast, if the short range interactions are disproportionately abundant, issues with the in situ ligation likely occurred in the experiment.

Loop Width Distribution Histogram

Above is a histogram of the loop widths greater than the minimum distance supplied in the parameters. Note that the loops smaller than the minimum distance have been filtered to make the histogram more interpretable (refer to the table above to see the proportion of very loops below the minimum distance, which are likely self-ligations).

Raw Read Stats

	K562_Rep1	K562_Rep3	K562_Rep2
Total_PETs	213,165,389	178,162,951	155,907,950
Mapped_unique_quality	227,379,220	178,511,506	166,531,145
Mapped_unique_quality_valid	84,853,173	60,184,588	63,563,804
Valid_Intra	73,198,912	52,708,198	55,118,481
Valid_Intra_<5Kb	18,352,064	14,680,263	13,808,130
Valid_Intra_5Kb-2Mb	45,942,066	32,366,438	35,517,487
Valid_Intra_>2Mb	8,904,782	5,661,497	5,792,864
Valid_Intra_anchor_5Kb-2Mb	3,506,603	2,720,245	3,542,961
HQ_Reads_In_Anchors	120,370,198	102,544,038	111,609,121

Proportional Read Stats

	K562_Rep1	K562_Rep3	K562_Rep2
Total_PETs	100.00	100.00	100.00
Mapped_unique_quality	106.67	100.20	106.81
Mapped_unique_quality_valid	39.81	33.78	40.77
Valid_Intra	34.34	29.58	35.35
Valid_Intra_<5Kb	8.61	8.24	8.86
Valid_Intra_5Kb-2Mb	21.55	18.17	22.78
Valid_Intra_>2Mb	4.18	3.18	3.72
Valid_Intra_anchor_5Kb-2Mb	1.65	1.53	2.27
Long_Range_Interactions	21.55	18.17	22.78

Number of Anchor Peaks

sample	npeaks
K562_Rep1	84598
K562_Rep3	84598
K562_Rep2	84598

The number of anchor peaks used in each sample. In lowly sequenced samples, these numbers may be low and be responsible for the lack of PETs mapping into loops.