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ScalePlex FAQs

Q1. When using ScalePlex, how does the ScaleRna pipeline assign sample barcodes to my ScalePlex samples?

See ScalePlex Overview for high-level concepts and ScalePlex Analysis for details on barcode assignment and sample barcode table requirements.

Q2. When using ScalePlex, how does the pipeline label ScalePlex barcodes with my cell barcodes?

See ScalePlex Analysis for details on ScalePlex assignment results, output files (e.g., assigned_scaleplex in .allCells.csv), and QC reports.

Q3. What do each of the ScalePlex failure modes mean?

See ScalePlex Analysis for explanations of ScalePlex assignment failure modes (Max Fail, Indeterminate, Enrich Fail, Unexpected) and troubleshooting guidance.

Q4. How do I process ScalePlex and non-ScalePlex samples within one library prep?

See ScalePlex Analysis for recommendations on processing mixed ScalePlex and non-ScalePlex samples.

Q5. When should I consider using fc instead of bg for ScalePlex assignment method?

See ScalePlex Analysis for guidance on choosing between background-based (bg) and fold-change (fc) assignment methods.

Need Help?

For more information, please contact support@scale.bio or visit our support website.