SCExecute Examples

Split BAM file based on STARsolo cell barcodes into indexed cell-specific BAM files, and for each, write the last ten aligned reads into a cell-specific SAM file. Run up to three commands at a time.

% bin/scExecute -r data/singlecell2_117.bam -G STARsolo -b data/barcodes.tsv -t 3 -i -C "samtools view {} | tail > test_{BAMBASE}_{BARCODE}_{CBINDEX}.sam"

See Also

SCExecute Home, Usage, Input Files, Cell Barcodes, Command/Template Substitution, Examples