2. Homeworks

Homeworks: day 1

Instructions

  • Process bulk ATAC-seq for PBMCs (GSE111013), perform QCs and compare them to single-cell QCs
  • Split bam file from mouse PBMCs scATACseq into bams / cell type using sinto
  • Make some celltype-specific pseudo-bulk bigwig tracks
  • Compare bulk and pseudo-bulk tracks in IGV; try to infer cell type for some of the cell clusters in scATACseq

Links:

Homeworks: day 2

  • Import counts from mouse E18 brain scATACseq (5K) (provided by 10X Genomics) in R and process them
  • Transfer annotations from PBMC 10X scRNAseq to PBMC 10X scATACseq (pre-processed scRNAseq available in data/MouseBrain/mPBMC_scRNAseq.rds)
  • Find genes associated to DA peaks and run GO over-enrichment / gene set enrichment analysis

Links:

Homeworks: day 3

  • Import, filter, normalize and cluster cells from the T-cell exhaustion dataset
  • Run chromVAR to identify TF activity in each cell cluster
  • Using knowledge on TFs used in different cell types, suggest cell cluster annotation of the dataset
  • Confirm this by computing gene activity scores and check known markers

Links: