What are the limitations of single cell sequencing?

Single-cell RNA sequencing (scRNA-seq) has several limitations, including biases in transcript coverage (to detect abundant transcripts), sequencing coverage, and low capture efficiency. These limitations contribute to scRNA-seq data having a higher degree of noise compared to bulk RNA-seq data. Moreover, the isolation procedure may cause unintentional stress on the cells, leading to changes in their behavior, characteristics and viability. Another limitation in single-cell analysis is that examining each individual cell within a population requires the high-throughput processing of hundreds of thousands to millions of single cells.