NGS ANALYSIS-scrna-seq

Basepair’s single cell RNA-seq analysis report includes boxplots that show the per-cell quality metrics.

• Genes/features detected shows the number of unique genes detected per cell. Very low unique genes can indicate empty droplets, while very high values can indicate droplets with two or more cells.
• UMI counts show the number of unique molecules detected per cell. Very low or high values indicate consequences similar to those of unique genes. 
• Mitochondrial proportion is the proportion of reads mapping to the mitochondrial genome. Values higher than 0.1 can indicate low-quality or dying cells.

Generally, you want to remove outliers and see cells clustering into one group. Although we provide sensible default filtering thresholds, we show the data before and after filtering so you can assess the results yourself.