run_arriba_starsolo_scRNAseq_piped.sh - Run STARSolo and Arriba on scRNA-seq FASTQ files to find integration sites. Makes two directories: starSolo_whitelist_stringent_output and arriba_output_solo_stringent which contain STAR and Arriba outputs respectively.
intSite_cellAssociation_scRNAseq.sh - Associate specific clusters with integration sites found with Arriba. Uses input from makeBarcodeFusionMatrix.sh and a TSV file of cell barcodes and their associated cluster from processed scRNA-seq data (cluster_barcode_IDs.tsv) generated in R.
findIntegrationPatterns.sh - Pulling out important information from Arriba output fusions.tsv to compare across samples.
makeBarcodeFusionMatrix.sh - Make a matrix of the number of fusion events for each cell based on Arriba output. Requires Arriba output fusions.tsv and R1 barcodes FASTQ files from CellRanger (/file/path/to/fastqs/*R1*).