CDN Workshop 2025

Day 1:June 9th 2025

1. scATAC-seq and scMultiome Analysis Overview

2. Basic scATAC-seq workflow

   • Main workflow steps
   • Data preprocessing

3. Combining samples and Quality Control

   • Merging multiple samples
   • Data quality control
   • Doublet detection

4. Normalization, Dimension reduction and Batch correction

   • Normalization
   • Dimension reduction
   • Batch correction

Day 2: June 16th 2025

5. snRNA and snATAC joint analysis and clustering

   • Joint analysis of snRNA and snATAC modalities
   • Validation of joint clustering
   • Compare to single-modality clustering

6. Gene-enhancer linking analysis

   • Why are gene-enhancer links useful?
   • Methods to link enhancers to target genes
   • Validation of gene-enhancer links

7. Differential chromatin accessibility analysis

   • What are DARs?
   • Methods to find cell type-specific DARs
   • Validation of peaks from DAR analysis

8. Motif enrichment analysis

   • What are motifs?
   • Significance of motifs
   • Representing motifs
   • Methods to identify motifs