Wang Xiaotao, Yue Feng
bioRxiv. 2023 Jan 20:2023.01.17.524475. doi: 10.1101/2023.01.17.524475.
With the continuous effort to improve the quality of human reference genome and the generation of more and more personal genomes, the conversion of genomic coordinates between genome assemblies is critical in many integrative and comparative studies. While tools have been developed for such task for linear genome signals such as ChIP-Seq, no tool exists to convert genome assemblies for chromatin interaction data, despite the importance of three-dimensional (3D) genome organization in gene regulation and disease.
Here, we present HiCLift, a fast and efficient tool that can convert the genomic coordinates of chromatin contacts such as Hi-C and Micro-C from one assembly to another, including the latest T2T genome. Comparing with the strategy of directly re-mapping raw reads to a different genome, HiCLift runs on average 42 times faster (hours vs. days), while outputs nearly identical contact matrices. More importantly, as HiCLift does not need to re-map the raw reads, it can directly convert human patient sample data, where the raw sequencing reads are sometimes hard to acquire or not available.
HiCLift is publicly available at https://github.com/XiaoTaoWang/HiCLift .
随着不断努力提高人类参考基因组质量以及越来越多个人基因组的产生，基因组组装之间的基因组坐标转换在许多整合和比较研究中至关重要。虽然已经开发了用于诸如ChIP-Seq等线性基因组信号的此类任务的工具，但尽管三维（3D）基因组组织在基因调控和疾病中很重要，但尚无用于转换染色质相互作用数据的基因组组装的工具。
在这里，我们展示了HiCLift，这是一种快速高效的工具，它可以将染色质接触（如Hi-C和Micro-C）的基因组坐标从一个组装转换到另一个组装，包括最新的T2T基因组。与将原始 reads 直接重新映射到不同基因组的策略相比，HiCLift的运行速度平均快42倍（从数天缩短至数小时），同时输出几乎相同的接触矩阵。更重要的是，由于HiCLift不需要重新映射原始 reads，它可以直接转换人类患者样本数据，而原始测序 reads 有时很难获取或无法获得。
