RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Schedule

The following schedule reflects a 7-day version of this course that is being hosted by Cold Spring Harbor in the Fall of 2021.

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 and curriculum. Instructor/student introductions.
  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   “Improved detection of DNA insertions with Absinthe” lecture
  13:00-14:00 1:00   Midday Break
  14:00-14:45 0:45   Oxford Nanopore Technology demo and tour
  14:45-16:00 1:15   “Single Cell Technologies and Applications” lecture
  16:00-16:30 0:30   Multi-omics protocols and lab “chalk talk”
  16:30-17:00 0:30   General open discussion
2 10:00-10:15 0:15   Introduction to the bioinformatics section
  10:15-11:30 1:15 0 Introduction to Cloud Computing and Cloud Set-up
  11:30-13:00 1:30   Command line warm up
  13:00-14:00 1:00   Midday Break
  14:00-15:00 1:00   Genomes, FASTA, FASTQ lecture
  15:00-16:00 1:00   Alignment fundamentals and practical
  16:00-17:00 1:00   BAM format and practical
3 10:00-11:00 1:00   Overview of variant calling
  11:00-11:45 0:45   Variant calling and variant interpretation practical
  11:45-12:00 0:15   Short Break
  12:00-13:00 1:00   Variant calling and variant interpretation practical
  13:00-14:00 1:00   “Importance of structural variants and value of long read sequencing” lecture
  14:00-15:00 1:00   Midday Break
  15:00-16:00 1:00   “Intro to RNA-sequencing and analysis” lecture
  16:00-16:15 0:15   Environment setup and tool installation lab
  16:15-17:00 0:45 1 Data inputs (reference genome, annotations, indexing, raw data) lab
4 10:00-10:30 0:30 2 Alignment lab
  10:30-11:30 1:00   Alignment Visualization lab
  11:30-12:00 0:30   Alignment QC lab
  12:00-13:00 1:00   “Statistics for count-based data and gene expression/differential expression analysis” lecture
  13:00-14:00 1:00   Midday Break
  14:00-15:00 2:00 3 StringTie, HTSeq, and spike-in analysis lab
  15:00-16:00 2:00   Differential expression analysis lab
  16:00-17:00 1:00   Wrap-up exercise with Q&A as needed
5 10:00-11:15 1:15   Differential expression visualization lab
  11:15-12:15 1:00   Differential expression pathway analysis lab
  12:15-13:00 0:45   Batch correction
  13:00-14:00 1:00   Midday Break
  14:00-16:30 2:30 4 Alignment free expression analysis with Kallisto lab
  16:30-17:00 0:30   Wrap-up exercise with Q&A as needed
6 10:00-11:00 1:00   “A complete reference genome improves analysis of human genetic variation” lecture
  11:00-12:00 1:00 8 “Intro to scRNAseq analysis” lecture
  12:00-13:00 1:00   Data generation, raw data format, data QC, Cell Ranger, and basic visualization in Loupe/VDJ browser lab
  13:00-14:00 1:00   Midday Break
  14:00-17:00 3:00   Seurat lab
7 10:00-11:00 1:00   “Variant Representation, Annotation, and Interpretation” lecture
  11:00-12:00 1:00   “Metagenomics and viromics” lecture
  12:00-13:00 1:00   Review multi-omics data generated during course
  13:00-14:00 1:00   Midday Break
  14:00-15:00 1:00   “Comprehensive Analysis of Single Cell Epigenomic Data” lecture
  15:00-16:00 1:00   “Epigenomics and NGS” lecture
  16:00-17:00 1:00   Wrap-up, Q&A, Evaluations