This repository contain resources and guides for the single-cell alternative splicing project.
The aim of this project is to identify regulated alternative splicing events between cell clusters from scRNA-Seq experiments. Here are the key objectives:
- Understand a typical scRNA-seq workflow (Smart-Seq vs 10X Genomics)
- Review current approaches to analyze single-cell alternative splicing and its limitations
- Process published scRNA-seq dataset to identify cell clusters
- Merge sequencing reads from cell clusters and compare alternative splicing landscape between clusters
- Identify enrichment in gene groups regulated by alternative splicing
Below are several resources that are useful for this project.
- scRNA-seq datasets
- Programs/packages for bioinformatics analysis
Some of the current tasks that can be done:
- Literature review of scRNA-seq workflows (Smart-Seq vs 10X Genomics)
- Literature review of single-cell alternative splicing analysis
- Download count matrix from scRNA-seq dataset
- Familiarize with Seurat package and R programming
- Import scRNA-seq matrix into R
- Carry QC on dataset and normalise+scale data
- Perform dimensional reduction (preferably UMAP/tSNE) and create clusters
- Identify cluster biomarkers and infer its cell type (if possible)
- Label tsne/UMAP plot with cell types annotated from main paper
- Plan pipeline for whippet analysis on clustered scRNA-seq transcriptome