---
title: "LongTREC OmicsBox Workshop - Nice 2024"
canonical: "https://help.biobam.com/space/BTP/3492937756/LongTREC%20OmicsBox%20Workshop%20-%20Nice%202024"
format: markdown
---
Welcome to the OmicsBox Workshop held as part of the LongTREC “Focus on Research” event in Nice, France!

**Date: 2024-03-10**

**Presenter: Fabian Jetzinger, LongTREC DC #12**

**Presentation: **[https://docs.google.com/presentation/d/1GhBqX_w9ip2aysgartK7y_D2ZcLY5dSmVVMd2Rke1tc/edit?usp=sharing](https://docs.google.com/presentation/d/1GhBqX_w9ip2aysgartK7y_D2ZcLY5dSmVVMd2Rke1tc/edit?usp=sharing)

# From long reads to functional insights: a bear use case 🐻 

## Prerequisites

Please take care of the following things before the course starts:

- ~~**Download and install the newest beta release of OmicsBox.**~~
  - ~~As these workshop pages are publicly available, the Beta-Release of OmicsBox that we will be working on is not linked here. You should have received an email with a link to the installer, as well as a License Key. If you have not received this email or if you cannot find it anymore, please let me know and I will send it again.~~
- **Download and install OmicsBox from here: **[Download OmicsBox - BioBam | Bioinformatics Made Easy](https://www.biobam.com/download-omicsbox/)
  - Please start OmicsBox once after installation to ensure the installation was successful. You have received the License Key via Mail. If there are any problems, please let me know!
- **Download the example data set here: **[https://drive.google.com/drive/folders/1TImxh7w5ZR0-gcnIwAgzl7hMza_rqwfj?usp=sharing](https://drive.google.com/drive/folders/1TImxh7w5ZR0-gcnIwAgzl7hMza_rqwfj?usp=sharing)

## Schedule

| **Timeslot** | **Duration** | **Topic** |
| --- | --- | --- |
| 14:30 - 15:00 | 30 min | Presentation: Introduction to OmicsBox |
| 15:00 - 15:25 | 25 min | [Hands-On Session 1: From raw reads to isoforms](https://biobam.atlassian.net/wiki/spaces/BTP/pages/3494215689) (minimap2, FLAIR, SQANTI3) |
| 15:25 - 15:35 | 10 min | Conclusion of Hands-On Session 1 |
| 15:35 - 15:40 | 5 min | Break |
| 15:40 - 15:50 | 10 min | Presentation: Quantification and Differential Expression |
| 15:50 - 16:05 | 15 min | [Hands-On Session 2: Quantification and Differential Expression ](https://biobam.atlassian.net/wiki/spaces/BTP/pages/3493888014)(IsoQuant, edgeR) |
| 16:05 - 16:15 | 10 min | Conclusion of Hands-On Session 2 |
| 16:15 - 16:20 | 5 min | Break |
| 16:20 - 16:45 | 25 min | Presentation: Functional Annotation and Analysis |
| 16:45 - 17:15 | 30 min | [Hands-On Session 3: Functional Annotation and Analysis](https://biobam.atlassian.net/wiki/spaces/BTP/pages/3495657474/Hands-On+Session+3%3A+Functional+Annotation) (BLAST, InterProScan, EggNog, GSEA) |
| 17:15 - 17:25 | 10 min | Conclusion of Hands-On Session 3 |
| 17:25 - 17:30 | 5 min | Questions, Feedback |