RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Schedule

Day Time Duration Module Topic
1 08:00-08:30 0:30 0 Registration and Breakfast
  08:30-09:00 0:30   Welcome and Introductions
  09:00-10:00 1:00   Lecture/Lab: Introduction to Cloud Computing
  10:00-10:30 0:30   Break
  10:30-12:00 1:30 1 Lecture: Introduction to RNA sequencing
  12:00-13:00 1:00   Lunch
  13:00-15:00 2:00   Inputs - References, Annotations, Indexing and Data
  15:00-15:30 0:30   Break
  15:30-16:00 0:30 2 Lecture: RNA-Seq Alignment and Visualization
  16:00-17:00 1:00   Adaptor Trimming, Alignment, QC and Visualization
  17:00-17:30 0:30   Break
  17:30-19:30 2:00   Integrated Assignment
2 08:00-08:30 0:30 3 Breakfast
  08:30-09:00 0:30   Lecture: Expression and Differential Expression
  09:00-10:00 1:00   Expression Estimation with StringTie & HTSeq
  10:00-10:30 0:30   Break
  10:30-12:00 1:30   Differential Expression and Visualization with Ballgown, edgeR
  12:00-13:00 1:00   Lunch
  13:00-13:30 0:30 4 Lecture: Introduction to Alignment Free Analysis
  13:30-14:30 1:00   Expression and DE analysis with kallisto and Sleuth
  14:30-15:00 0:30   Break
  15:00-17:00 1:00 5 Alternative Expression Analysis - Isoform Analysis
  17:00-17:30 0:30   Break
  17:30-19:30 2:00   Integrated Assignment
3 08:00-08:30 0:30 6 Breakfast
  08:30-10:00 1:30   Lecture: Transcriptome Assembly
  10:00-10:30 0:30   Break
  10:30-12:00 1:30   De novo RNA-Seq Assembly and Analysis Using Trinity
  12:00-13:00 1:00   Lunch
  13:00-14:30 1:30 7 Lecture: Transcriptome Annotation
  14:30-15:00 0:30   Break
  15:00-17:00 2:00   Transcript Annotation with Trinotate
  17:00-17:30 0:30   Survey and Closing Remarks