Isoform Project

Goal: quantify and describe the presence of different gene isoforms (variant transcripts of a gene produced by alternative splicing) in scRNA-seq data

R Notebook for Visualization & Quantification

• Creates random sampling of FASTQ files for cells within a specific subclass (for input in STAR script)
• Merges BAM files (the outputs of STAR script) for later visualization and quantification at the subclass-level
• Uses Bioconductor functions to set up and plot a figure visualizing the following:
  1. read coverage
  2. junctions (i.e., sashimi plot)
  3. gene isoform models

Example STAR Script for Read Alignment

• Given FASTQ files, processed genome index directory, and genome annotation file (.gtf or .gff), creates scripts which will produce coordinate-sorted BAMs for gene quantification
• More details and documentation here