RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Schedule

Each day runs from 10:00 AM Eastern to 5:00 PM Eastern

Day Time (ET) Duration Module Topic
1 10:00-10:15 0:15   Introduction to the course
  10:15-11:15 1:00   “Overview of Next-generation Short Read Sequencing Technologies and Methods” lecture
  11:15-12:15 1:00   “PacBIO and Oxford Nanopore Long read sequencing” lecture
  12:15-13:00 0:45   “Single Cell Sequencing Technology and Applications” lecture
  13:00-14:00 1:00   Midday Break
  14:00-15:00 1:00   “Epigenomics and NGS” lecture
  15:00-15:15 0:15   Introduction to bioinformatics instructors
  15:15-16:00 0:45 0 Introduction to Cloud Computing and Cloud Set-up
  16:00-17:00 1:00   Command line warm up
2 10:00-11:00 1:00   “Intro to RNA-sequencing and analysis” lecture
  11:00-11:30 0:30   Environment setup and tool installation lab
  11:30-12:00 0:30   Mini-lectures on FASTA/FASTQ/GTF and Indexing
  12:00-13:00 1:00 1 Data inputs (reference genome, annotations, indexing, raw data) lab
  13:00-14:00 1:00   Midday Break
  14:00-14:30 0:30   Mini-lectures on alignment and SAM/BAM/BED formats
  14:30-15:00 0:30 2 Alignment lab
  15:00-16:00 1:00   Alignment Visualization lab
  16:00-16:30 0:30   Alignment QC lab
  16:30-17:00 0:30   Wrap-up exercise with Q&A as needed
3 10:00-11:00 1:00   “Abundance estimation, HTSeq and differential expression” lecture
  11:00-13:00 2:00 3 StringTie, HTSeq, and spike-in analysis lab
  13:00-14:00 1:00   Midday Break
  14:00-16:00 2:00   Differential expression analysis lab
  16:00-17:00 1:00   Wrap-up exercise with Q&A as needed
4 10:00-11:15 1:15   “Statistics for count-based data and gene expression/differential expression analysis” lecture
  11:15-13:00 1:45   Differential expression visualization lab
  13:00-14:00 1:00   Midday Break
  14:00-14:30 0:30   Differential expression pathway analysis lab
  14:30-16:30 2:00 4 Alignment free expression analysis with Kallisto lab
  16:30-17:00 0:30   Wrap-up exercise with Q&A as needed
5 10:00-11:00 1:00   “Intro to scRNAseq analysis” lecture
  11:00-13:00 2:00 8 Data generation, raw data format, data QC, Cell Ranger, and basic visualization lab
  13:00-14:00 1:00   Midday Break
  14:00-16:30 2:30   Seurat lab
  16:30-17:00 0:30   Wrap-up exercise with Q&A as needed