scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Fig 2
Example QC plots that can be created using output from scPipe to assess data quality both within and between experiments.
Within experiment displays include (A) a bar plot illustrating the overall cell barcode matching results to assess sequencing accuracy across all samples and (B) a stacked bar plot showing the mapping rate, separated into reads that map to exon, intron and ERCCs and those that are ambiguously mapped, map elsewhere in the genome and are unaligned for each cell in an experiment (ordered by exon mapping rate). Between experiment displays include (C) a stacked bar plot showing the cell barcode matching results from panel (A) from multiple experiments and (D) a ridgeline plot presenting the distribution of proportions of non-mitochondrial read counts for cells across multiple experiments.