RNA-Seq data analysis
Using the Unix shell and R
Schedule
Block A: Computing skills and genomics data files
| Date | Topic & link |
|---|---|
| 2023-07-14 | Introduction |
| 2023-07-21 | The Ohio Supercomputer Center (OSC) |
| 2023-07-28 | VS Code & Unix shell (part I) |
| 2023-08-04 | Unix shell (part II) |
| 2023-08-11 | FASTQ files |
| 2023-08-18 | Reference genome files (FASTA and GTF) |
| 2023-08-25 | Overview of next steps, variables, and loops |
| 2023-09-01 | Shell scripting |
| 2023-09-08 | Software at OSC |
| 2023-09-15 | Slurm batch jobs |
Block B: From reads to counts
| Date | Topic & link |
|---|---|
| 2023-09-22 | Read quality control with FastQC |
| 2023-10-13 | Quality and adapter trimming with TrimGalore |
Block C: Count table analysis
| Date | Topic & link |
|---|---|
| 2024-04-09 | Gene count table analysis part I |
| 2024-04-23 | Gene count table analysis part II |