SCExecute generates cell-barcode specific BAM files from aligned, aggregate single-cell sequencing data, executing a user-provided command on each barcode-stratified BAM file. Unlike other tools, SCExecute generates cell-barcode specific BAM files in batches to avoid file-system and memory constraints, and manages the execution of the user-provided commands on multiple processes to improve throughput. Cell-barcodes can be extracted from read-names or BAM-file tags populated by a variety of tools, included STARsolo and UMI-tools, and can be restricted to barcodes of interest. Implemented in Python3 using the PySAM package and distributed for Linux, MacOS, and Python environments, SCExecute builds on other NGS tools from the Horvath lab, including SCReadCounts.

SCExecute is available as a self-contained binary package for 64-bit Linux systems, as Python source, and MacOS (Darwin). The self-contained binary package is appropriate for most Linux and MacOS users. The pythonic version requires pysam, numpy and scipy along with other packages (See the install instructions for more details).

SCExecute provides explicit configuration for alignments barcoded through STARsolo and UMItools. Additional cellular barcode extraction logic can be configured software, based on BAM file tags or RNA sequence name and delimited tokens or regular expressions (see Cell Barcode documentation).

Setup:

• Download
• Install

Usage:

• SCExecute

Other:

• Input Files
• Cell Barcodes
• Command/Template Substitution

Examples

Please cite:

• Edwards, N., Dillard, C., Prashant, N.M., Liu, H., Yang, M., Ulianova, E., and Horvath, A. SCExecute: custom cell barcode-stratified analyses of scRNA-seq data. Bioinformatics (2022).