, printed on 08/12/2020
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].