FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data.

ABSTRACT:

Summary

Single molecule footprinting profiles the heterogeneity of TF occupancy at cis-regulatory elements across cell populations at unprecedented resolution. The single molecule nature of the data in principle allows for observing the footprint of individual transcription factors and nucleosomes. However, we currently lack algorithms to quantify these occupancy patterns of chromatin binding factors in an automated way and without prior assumptions on their genomic location. Here we present FootprintCharter, an unsupervised tool to detect and quantify footprints for transcription factors (TFs) and nucleosomes from single molecule footprinting data. After detection, TF footprints can be labeled with orthogonal motif annotations provided by the user. FootprintCharter allows for the

SUBMITTER: Barzaghi G 

PROVIDER: S-EPMC12490827 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature