Question: What is the recommended sequencing depth for Single Cell 3' Gene Expression libraries?
Answer: For new samples, we typically recommend sequencing ~50k read pairs/cell. The sequencing depth for each experiment, however, will depend on the (1) sample type and (2) the experimental question being addressed.
The 'Sequencing Saturation' metric reported in the Cell Ranger run summary can be used to optimize sequencing depth for specific sample types. (This metric was named cDNA PCR Duplication in Cell Ranger 1.1 or earlier.)
- For instance, with 50k reads/cell for RNA rich cells such as cell lines, you'll reach around 30-50% sequencing saturation depending on the total RNA that is expressed per cell. This may be sufficient to cluster your sub-populations of interest during the analysis.
- If you are interested in identifying as many genes as possible in your sample, you may want to sequence deeper to reach around 90% sequencing saturation level.
For more information, see the Technical Note Resolving Cell Types as a Function of Read Depth and Cell Number.
Products: Single Cell 3', VDJ