, printed on 08/12/2020
For sequencing Targeted Single Cell Gene Expression libraries, use the same sequencing parameters recommended for their parent Single Cell Gene Expression or Single Cell Immune Profiling libraries.
The minimum recommended sequencing depth is 2,000 read pairs per cell for pre-designed panels. When using Custom Panels, optimization of sequencing depth may be required based on panel size and expression levels of panel genes. The Cell Ranger targeted-depth tool can recommend sequencing depth for a Targeted Gene Expression library enriched from an existing whole transcriptome library analyzed with Cell Ranger (or enriched from a similar library).
Coming soon: sequencing guidelines for Targeted libraries prepared from Spatial Gene Expression libraries will be available soon. For more information, please contact [email protected].