This study investigates different read depths of biological replicates for reproducibility and benchmarking of Capture Hi-C assays.

This study investigates different read depths of biological replicates for reproducibility and benchmarking of Capture Hi-C assays. We generated two replicates of Capture Hi-C libraries using SUM44 breast cancer cells. These were first profiled on a single sequencing lane, and assessed for concordance between interactions. Next, same replicates were profiled on a second sequencing lane thereby resulting in two sets of replicates. Each set was pooled together and combined replicates were compared against each other and contrasted to single lane experiments. We prioritise interactions which are read depth dependent and identify experimental noise specific to individual replicates.