Transcriptome Analysis for Non-Model Organisms (ONLINE LIVE TRAINING) PrerequisitesNew
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.
- 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
- 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.
Bioinformatics, Functional genomics, Data visualisation, Transcriptomics, Data handling, Data mining, RNA-seq
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
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
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.
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 |
- 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
5
Once a year
- Introduction to R for Biologists (ONLINE LIVE TRAINING)
- CRUK: Data Carpentry in R
- Bulk RNA-seq analysis (ONLINE LIVE TRAINING)
- Single-cell RNA-seq analysis (ONLINE LIVE TRAINING)
- Analysis of DNA Methylation using Sequencing (IN-PERSON)
Events available