Day 2 - ryandkuster/EPP_575_RNA_25 GitHub Wiki
Agenda
| Time | Lecture | Lab | Instructor |
|---|---|---|---|
| 9:00 | Catch-up | ||
| 9:10 | 05 Loops | SWC 5 | Zane |
| 9:20 | |||
| 9:30 | |||
| 9:40 | 06 Shell Scripts | SWC 6 | Zane |
| 9:50 | |||
| 10:00 | |||
| 10:10 | 10 minute break | :coffee: | |
| 10:20 | 07 Finding Things | SWC 7 | Trinity |
| 10:30 | |||
| 10:40 | |||
| 10:50 | File formats: gff3 | ||
| 11:00 | Introduction to RNA-Seq | Ryan | |
| 11:10 | |||
| 11:20 |
Day 2 Assignment:
Send the following to [email protected] by the end of the day. If you have encountered any issues with accessing materials or command line functionality, please also indicate this in the email.
Thinking about the data you work with (or plan to work with) in your research, pick three commands or concepts (e.g. for-loops, bash scripts) from the command line materials we’ve covered so far. How might you use these commands to summarize your data or work with your data?
Based on the “Qalba_4.3.0.HapA.genes.Chr01.gff3” file in EPP_575_RNA/data/practice_data, the third column is the type of feature. Count the number of rows where this field is equal to “CDS”. There are multiple ways of doing this, so think about how to isolate only the information you want.