Prerequisites
Linux
LinuxJedi
HPC
RNAseq
Program
- Transcrits assembly with Trinity
- Checking assembly quality
- Differential expression analysis of transcrits (DE)
- Funtional annotation of transcrits with Trinotate
- Codants regions prediction with TransDecoder
Learning objectives
- Manipulate tools available for assemblies analysis
- Study differential expression by using RNAseq data without a reference genome
- Visualize diversity metrics in assemblies approaches
- Annotate transcrits to know functions of genes
Training material
- [Intro] Training introduction : see
- [Survival] Basic commands in SLURM : see
- Reads quality slides : see
- [ Practice 1. ] Checking Reads Quality see
- Assembly slides : see
- [ Practice 2. ] Assembling transcriptome from RNA-seq see
- Assesment slides : see
- [ Practice 3. ] Assessing transcriptome assembly quality see
- Annotation slides : see
- [ Practice 5 . ] Functional annotation see
- Differential Expression slides : see
- [ Practice 4.] Differential Expression Analysis (DE) see
Instructors
- Erwan Corre (EC) - corre@sb-roscoff.fr
- Julie Orjuela-Bouniol (JO) - julie.orjuela@ird.fr
- Christine Tranchant-Dubreuil (AD) - christine.tranchant@ird.fr
- Aurore Comte (AC) - aurore.comte@ird.fr
- Stephanie SIDIBE BOCS (SSB) - stephanie.sidibe-bocs@cirad.fr
- David Lopez (DL) - david.lopez@cirad.fr
Trainings
| Date |
Location |
Topics |
Participants |
Instructors |
Links |
Units |
| 2019 |
Montpellier, France |
Introduction to assembly and annotation of transcrits |
15 |
EC JO CT AC SSB DL |
|
SOUTHGREEN ABiMS - IFB aliance |
