scATAC_workshop_2025

CDN Workshop 2025

Day 1:June 9th 2025

1. scATAC-seq and scMultiome Analysis Overview [Recording]

Recording for Sessions 2-4

1. Basic scATAC-seq workflow
   • Main workflow steps
   • Data preprocessing
2. Combining samples and Quality Control
   • Merging multiple samples
   • Data quality control
   • Doublet detection
3. Normalization, Dimension reduction and Batch correction
   • Normalization
   • Dimension reduction
   • Batch correction

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Day 2: June 16th 2025

1. snRNA and snATAC joint analysis and clustering [Recording]
   • Joint analysis of snRNA and snATAC modalities
   • Validation of joint clustering
   • Compare to single-modality clustering
2. Gene-enhancer linking analysis [Recording]
   • Why are gene-enhancer links useful?
   • Methods to link enhancers to target genes
   • Validation of gene-enhancer links
3. Differential chromatin accessibility analysis [Recording]
   • What are DARs?
   • Methods to find cell type-specific DARs
   • Validation of peaks from DAR analysis
4. Motif enrichment analysis
   • What are motifs?
   • Significance of motifs
   • Representing motifs
   • Methods to identify motifs