SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells

Motivation Cell type-specific activities of cis-regulatory elements (CRE) are central to understanding gene regulation and disease predisposition. Single-cell RNA 5 ' end sequencing (sc-end5-seq) captures the transcription start sites (TSS) which can be used as a proxy to measure the activity of transcribed CREs (tCREs). However, a substantial fraction of TSS identified from sc-end5-seq data may not be genuine due to various artifacts, hindering the use of sc-end5-seq for de novo discovery of tCREs. Results We developed SCAFE-Single-Cell Analysis of Five-prime Ends-a software suite that processes sc-end5-seq data to de novo identify TSS clusters based on multiple logistic regression. It annotates tCREs based on the identified TSS clusters and generates a tCRE-by-cell count matrix for downstream analyses. The software suite consists of a set of flexible tools that could either be run independently or as pre-configured workflows. Availability and implementation SCAFE is implemented in Perl and R. The source code and documentation are freely available for download under the MIT License from . Docker images are available from . The submitted software version and test data are archived at and , respectively. Supplementary information are available at Bioinformatics online.