Fig. 1

ScRNAbox analysis workflow. The scRNAbox pipeline provides two analysis tracks: 1) standard scRNAseq and 2) HTO scRNAseq. A Standard scRNAseq data is prepared by sequencing each sample separately, resulting in distinct FASTQ files for each sample. B HTO scRNAseq data is produced by tagging the cells from each sample with unique oligonucleotide “Hashtag” conjugated antibodies (HTO). Tagged cells from each sample are then pooled and sequenced together to produce a single FASTQ file. Sample-specific HTOs are used to computationally demultiplex samples downstream. C Steps of the scRNAbox pipeline workflow. Steps are designed to run sequentially and are submitted using the provided bash scripts through the command line. scRNAbox takes FASTQ files as input into Step 1; however, the pipeline can be initiated at any step which takes the users processed data as input