Tutorial

Keywords

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

Authors

• Nicolas Delhomme (@delhomme)
• Bastian Schiffthaler (@bastian)

Type

• Practical

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

Description

This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided.

Aims

Irrelevant here, see above

Prerequisites

• Irrelevant here, see above

Target audience

Irrelevant here, see above

Learning objectives

• Irrelevant here, see above

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

Materials

• Tutorial PDF: Generated from the companion R package
• Code source from chapter 4: R code extracted from Chapter 4 to avoid too much typing from the trainees
• Code source from chapter 5: Same as above for chapter 5,
• Code source from chapter 6: chapter 6
• Code source from chapter 7: and chapter 7.
• Installation HTML document: A set of instructions for trainees to install the R package and its dependencies prior to the course on their own laptops.
• Installation R script: the R script which knitted output is the HTML file above

Data

• The data availability is described in the Dataset section

Timing

Irrelevant here, see above

Content stability

Stable. The data and analyses are public. The analysis has been conducted using the Populus trichocarpa sister species and might only get updated once the Populus tremula genome sequence and annotation are released, which may happen by the end of 2015.

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

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