CUT&RUNTools 2.0: A pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis.

ABSTRACT:

Motivation

Genome-wide profiling of transcription factor binding and chromatin states is a widely-used approach for mechanistic understanding of gene regulation. Recent technology development has enabled such profiling at single-cell resolution. However, an end-to-end computational pipeline for analyzing such data is still lacking.

Results

Here, we have developed a flexible pipeline for analysis and visualization of single-cell CUT&Tag and CUT&RUN data, which provides functions for sequence alignment, quality control, dimensionality reduction, cell clustering, data aggregation, and visualization. Furthermore, it is also seamlessly integrated with the functions in original CUT&RUNTools for population-level analyses. As such, this provides a valuable toolbox for the community.

Availability and implementation

https://github.com/fl-yu/CUT-RUNTools-2.0.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Yu F 

PROVIDER: S-EPMC8696090 | biostudies-literature |

REPOSITORIES: biostudies-literature