QC Reports

In this folder hierarchy, we hub all QC Reports from HiChIP that we can get our hands on to facilitate comparisons. We’ve pre-categorized current reports into libraries that look good and bad. Additionally, we’ve done some analyses to determine some noteworthy features of the HiChIP experiment/sequencing run (see below). Have more reports to contribute? We’d greatly appreciate it if you submitted a pull request or emailed Caleb with your report!

When planning a HiChIP experiment and sequencing run, we consider three key factors: 1) cellular input, 2) read length, and 3) read count.


A paper published in late 2017 in Nature Genetics used K27ac for HiChIP. See the loop call QC reports from hichipper here:

Variable Cell Input

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While each sample looks mostly successful in terms of long range interactions, we observe significant heterogeneity in ChIP efficacies as the % of reads in anchors varies considerably within sample batches.

Variable Read Length (75bp versus 100bp)

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The original HiChIP paper only sequenced using 75 bp PE reads for all samples. To infer the impact of read length, we sequencing a high quality library at 100 bp PE reads and then trimmed these reads to 75 bp. From our analyses, this causes a 5-6% reduction in mappable interactions and ~12-13% reduction in reads in loops. Depending on the availability of sequencing technology, we suggest using 75 bp reads with more depth may be a more economical experimental strategy.

Downsampled (Variable Read Depth)

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Three samples were created from random downsampling of the GM12878 HiChIP experiment with 1 million, 500,000 and 250,000 reads. As the proportion of long range interactions remains relatively constant, we suggest that a relatively small number of reads may be sufficient to determine library quality before performing a deeper sequencing run. This comparison is just a reorganization of data in the Good/Mumbach_etal/ folder. The original SRR files shown here include SRR3467183 (10 million), SRR3467185 (5 million), and SRR3467187 (1 million).