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Schedule |
## RNA-seq Bioinformatics
Introduction to bioinformatics for RNA sequence analysis
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The following is a representative schedule for a 7-day version of this course that was hosted by Cold Spring Harbor in the Fall of 2021.
Each day ran 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 |