{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T17:13:18Z","timestamp":1777396398896,"version":"3.51.4"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,30]],"date-time":"2022-11-30T00:00:00Z","timestamp":1669766400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"McCormick Genomic and Proteomic Center at George Washington University","award":["MGPC2022"],"award-info":[{"award-number":["MGPC2022"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>In single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are not sufficiently supported by available tools designed for high-throughput sequencing data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce SCExecute, which executes a user-provided command on barcode-stratified, extracted on-the-fly, single-cell binary alignment map (scBAM) files. SCExecute extracts the alignments with each cell barcode from aligned, pooled single-cell sequencing data. Simple commands, monolithic programs, multi-command shell scripts or complex shell-based pipelines are then executed on each scBAM file. scBAM files can be restricted to specific barcodes and\/or genomic regions of interest. We demonstrate SCExecute with two popular variant callers\u2014GATK and Strelka2\u2014executed in shell-scripts together with commands for BAM file manipulation and variant filtering, to detect single-cell-specific expressed single nucleotide variants from droplet scRNA-seq data (10X Genomics Chromium System).<\/jats:p>\n                  <jats:p>In conclusion, SCExecute facilitates custom cell-level analyses on barcoded scRNA-seq data using currently available tools and provides an effective solution for studying low (cellular) frequency transcriptome features.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SCExecute is implemented in Python3 using the Pysam package and distributed for Linux, MacOS and Python environments from https:\/\/horvathlab.github.io\/NGS\/SCExecute.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac768","type":"journal-article","created":{"date-parts":[[2022,11,30]],"date-time":"2022-11-30T15:09:05Z","timestamp":1669820945000},"source":"Crossref","is-referenced-by-count":6,"title":["SCExecute: custom cell barcode-stratified analyses of scRNA-seq data"],"prefix":"10.1093","volume":"39","author":[{"given":"Nathan","family":"Edwards","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular & Cellular Biology, Georgetown University , Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Dillard","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Medicine, McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George 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