hichipper QC report

2017-12-29

hichipper, version 0.7.1.

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.