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Mon 1 Mar - Fri 5 Mar 2021
09:30 - 17:30

Venue: Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

Provided by: Bioinformatics


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Transcriptome Analysis for Non-Model Organisms (ONLINE LIVE TRAINING)
PrerequisitesNew

Mon 1 Mar - Fri 5 Mar 2021

Description

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms.

This course provides an overview of modern applications of transcriptome sequencing and popular tools, and algorithms, for exploring transcript reconstruction and expression analysis in a genome-free manner.

Attendees will perform quality assessment and upstream analysis of both Illumina and long reads single molecule sequencing data; the derived transcriptomes will be compared, annotated and used as reference for quantifying transcript expression, leveraging on Bioconductor tools for differential expression analysis. Additional methods will be explored for characterising the assembled transcriptome and revealing biological findings.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Prerequisites
  • This workshop is aimed primarily at researchers that have basic bioinformatics skills and are pursuing RNA-Seq projects in non-model organisms.
  • Basic experience of command line UNIX. Sufficient UNIX experience might be obtained from the following UNIX tutorial
  • Basic knowledge of the R syntax. We recommend either attending Introduction to R for biologists, or working through the materials of the now discontinued Data Carpentry in R courses before attending this course.
Sessions

Number of sessions: 5

# Date Time Venue Trainers
1 Mon 1 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter) Nico Delhomme,  Bastian Schiffthaler
2 Tue 2 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter) Nico Delhomme,  Bastian Schiffthaler
3 Wed 3 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter) Nico Delhomme,  Bastian Schiffthaler
4 Thu 4 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter) Nico Delhomme,  Bastian Schiffthaler
5 Fri 5 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter) Nico Delhomme,  Bastian Schiffthaler
Topics covered

Bioinformatics, Functional genomics, Data visualisation, Transcriptomics, Data handling, Data mining, RNA-seq

Objectives

After this course you should be able to:

  • Describe the challenges associated with de-novo transcriptome assembly, of either short or long read data
  • Compare assemblies derived from Illumina and third generation sequencing data
  • Assess the quality of a de-novo assembly
  • Describe the annotation process of a de-novo assembly
  • Perform pseudo-mapping and quantification of expression using state of the art solutions
  • Utilise some of the tools available in Bioconductor for downstream analysis such as e.g. differential expression analysis
Aims

During this course you will learn about:

  • The use of third generation sequencing for transcript reconstruction and expression analysis in non-model organisms
  • de novo assembly, assembly QC and expression quantitation
  • Differential expression analysis using Bioconductor
  • Functional annotation and functional enrichment studies
Format

Online only. Presentations will be held in Zoom and recorded. Demonstrations and practicals will also be held in Zoom but some of it could be done asynchronously in smaller groups.

Timetable

This is subject to change in line with the online training schedule.

Day 1 Topics - High Throughput Sequencing, 2nd generation
Session 1 Welcome to the course
Session 2 High Throughput Sequencing lecture
Morning coffee break
Session 3 Data Processing Workflow lecture
Session 4 Data pre-processing discussion
Lunch break
Session 5 Data Description
Session 6 Hands-on practical data pre-processing
Afternoon coffee break incorporated in Session 6 (practical)
Session 7 Feedback and Daily Assessment
Day 2 Topics - NGS data de-novo transcriptome assembly
Session 1 Revisions Session
Session 2 Hands-on practical data pre-processing (Input QC tutorial)
Morning coffee break incorporated in Session 2 (practical)
Lunch break
Session 3 De-novo transcriptome assembly lecture and tutorial (Input Transcriptome Assembly)
Afternoon coffee break incorporated in Session 3 (lecture and tutorial)
Session 4 Feedback and Daily Assessment
Day 3 Topics - Third(!) generation sequencing, de-novo transcriptome assembly, assessment and evaluation
Session 1 Revision Session
Session 2 De-novo transcriptome assembly lecture - 3rd generation sequencing!
Morning coffee break
Session 3 De-novo transcriptome assembly - revisited
  Lunch break
Session 4 Assembly evaluation (Transcriptome evaluation)
Session 5 Functional annotation (Transcriptome annotation)
Afternoon coffee break incorporated in Session 5
Session 6 Feedback and Daily Assessment
Day 4 Topics - Transcript quantification and Differential Expression
Session 1 Revision Session
Session 2 Pseudo-alignment lecture
Morning coffee break
Session 3 Hands-on practical - Pseudo alignment (Bash scripting and looping tutorial)
Session 4 Statistical concerns lecture
  Lunch break
Session 5 Statistical concerns lecture
Session 6 Differential Expression analysis setup - until the Exploratory analysis and visualisation (included)
Afternoon coffee break
Session 7 Differential Expression lecture
Session 8 Feedback and Daily Assessment
Day 5 Topics - Quantification and Differential expression analysis
Session 1 Revisions Session
Session 2 Differential Expression analysis setup - until the Exploratory analysis and visualisation (included)
Morning coffee break incorporated in Session 2
Session 3 Differential Expression lecture
Lunch break
Session 4 Differential Expression lecture
Session 5 Differential Expression analysis practical
Afternoon coffee break incorporated in Session 5 (practical)
Session 6 Final revision session and Feedback
Registration fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

5

Frequency

Once a year

Related courses
Theme
Specialized Training

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