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Assembling and functionally annotating a de-novo transcriptome from RNA-seq data


This course offers an introduction to pre-processing, assembling and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms.

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