MACS3, Peak Caller with Single-Cell Resolution
Tao Liu (Roswell Park Alliance Foundation)
To maintain the established infrastructure and optimize the current features of the popular peak caller MACS for gene regulation studies, while focusing on building the data structure and features for single-cell data analysis.
MACS has been an essential software for calling peaks from ChIP-seq, DNase-seq, and ATAC-seq experiments in gene regulation studies. Initially published in 2008 and later updated to MACS2 and MACS3, this open-source tool has enjoyed an annual increase in citations which totaled over 10,000. With the recent development of computation, bioinformatics, and genomics technologies, especially single-cell assays, MACS needs critical updates to maintain and improve its utilities. This proposal aims to hire a dedicated postdoc researcher or programmer to focus on implementing the data structure and to build flexible peak-calling routines for data from single-cell DNA sequencing technologies, including but not limited to single-cell ATAC-seq and single-cell Cut&Run. This proposal’s aims will make MACS3 imminently valuable to the gene regulation community, especially those adopting single-cell sequencing technologies on tissues and tumors, and enable MACS3 to become interoperable with other bioinformatics tools for sustained community engagement.