Nicolas Delhomme and Bastian Schiffthaler

Nicolas Delhomme and Bastian Schiffthaler

Keywords

FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Authors

  • @delhomme
  • @bastian

| Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references |

Description

This merely lists the various courses at which we taught RNA-Seq data
pre-processing and analysis:

October 2014 EMBO course

Aims

Detailled in the corresponding courses:
1. October 2014 EMBO course

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Prerequisites

Detailled in the corresponding courses:
1. October 2014 EMBO course

Target audience

  • From undergrade on, provided that the prerequisites above are fulfilled

Learning objectives

  1. Introduction
  2. Quality Control
  3. Alignment
  4. Annotation
  5. Expression-estimation
  6. Differential-expression
    • What is a differential expression analysis
    • How to assess the quality (the biological meaningfulness) of the count data
    • What is a confounding factor
    • How to identify a confounding factor
    • How to block a confounding factor

| Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references |

Materials

Detailled in the corresponding courses:
1. October 2014 EMBO course

Data

### Description
Uses the dataset Robinson, Delhomme et al., 2014

Availability

Detailed in the dataset Robinson, Delhomme et al., 2014

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Technical requirements

  • Best is to use our Docker (a self contained environment) based on the Bioconductor NGS Docker that can be used to setup the course machines (physical or in the cloud)
  • Otherwise:
    • a UNIX OS
    • FastQC
    • SortMeRna (>= 1.9)
    • Trimmomatic (>=0.32)
    • STAR (>=2.4.0)
    • R (>=3.1), Bioconductor(>=3.0)

Literature references

  • Robinson, Delhomme et al.
  • SortMeRna
  • Trimmomatic
  • STAR
  • Bioconductor

| Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references |

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Authors: @delhomme, @bastian

Nicolas Delhomme and Bastian Schiffthaler https://tess.elixir-europe.org/materials/nicolas-delhomme-and-bastian-schiffthaler This merely lists the various courses at which we taught RNA-Seq data RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming