Fig. 1
From: scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data
scruff package workflow. a Schematic diagram of each step in scruff. b scruff workflow. Reads from FASTQ files are first demultiplexed into cell-specific FASTQ files according to their cell barcodes. During this process, UMI tags are appended to the read header of the transcript sequences. scruff applies the Subread [18] algorithm for sequence alignment for each cell. Next, reads mapped to genes are counted according to their UMI. Within each gene, reads with identical UMI (red dashed circle) are counted only once. QC metrics are collected at each of these steps and are used for visualization of data quality