Schedule
For the CBW Sept 2021 RNA-seq course, please refer to the CBW schedule.
The following schedule reflects a 5-day version of this course that was hosted by Cold Spring Harbor in Fall of 2020.
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 |