What are the key bioinformatic QC metrics for SeekOne DD Multiome Methylation + RNA data?

Answer:
The SeekOne DD Single-Cell Multiome Methylation + RNA workflow simultaneously profiles transcriptomic and DNA methylation information from the same single cell. RNA-seq QC metrics generally follow the same interpretation standards as conventional SeekOne DD 3’ scRNA-seq workflows. In addition to transcriptomic QC, methylation-specific QC metrics are critical for evaluating:

• EM-seq conversion efficiency
• Methylation signal fidelity
• Genome mapping quality
• Genome-wide CpG coverage
• False-positive and false-negative methylation risks
• Library structural integrity 

The methylation modality itself does not perform an independent cell-calling process. Cell calling is based on transcriptomic data, and methylation QC interpretation should therefore be integrated with RNA QC results.

QC reports generated by the SeekSoulMethyl pipeline are primarily divided into:

• RNA sequencing QC metrics
• RNA cell-level QC metrics
• Methylation sequencing QC metrics
• Methylation mapping QC metrics
• Methylation cell-level QC metrics 

1. RNA QC Metrics

Follow the same interpretation standards as conventional SeekOne DD 3’ scRNA-seq workflows.

2. Sequencing QC Metrics (MET)

3. Mapping and Methylation QC Metrics (MET)

4. Cell-Level QC Metrics (MET)