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Instructor-led course

Provided by: Bioinformatics


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Analysis of small RNA-seq data
PrerequisitesNew


Description

This course focuses on methods for the analysis of small non-coding RNA data obtained from high-throughput sequencing (HTS) applications (small RNA-seq). During the course, approaches to the investigation of all classes of small non-coding RNAs will be presented, in all organisms.

Day 1 will focus on the analysis of microRNAs and day 2 will cover the analysis of other types of small RNAs, including Piwi-interacting (piRNA), small interfering (siRNA), small nucleolar (snoRNA) and tRNA-derived (tsRNA).

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book 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 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
Topics covered

Bioinformatics, Data handling, Data mining, Data visualisation, Functional genomics

Objectives

After this course you should be able to:

  • Design a useful and statistically powerful small RNA-seq experiment
  • Understand the theory of count-based data analysis and differences for small RNA-seq
  • Perform a full analysis of a small RNA-seq dataset from raw data to stats
  • Predict microRNA targets for subsequent validation
  • Locate and characterise piRNA precursors
  • Identify genomic loci with high abundance of small RNAs
Aims

During this course you will learn about:

  • Analysis of small RNA-seq data (QC, trimming, mapping)
  • Appropriate statistical techniques for HTS data analysis
  • Prediction of miRNA binding sites in genome-wide data sets
  • Identification of other classes of small RNAs (piRNAs, siRNAs, snoRNAs, tsRNAs)
Format

Presentation and demonstrations

Timetable

Day 1 Topics Speaker(s)
09:30 - 10:30 microRNA biogenesis, function and profiling, differences (and similarities) to other non-coding RNAs Anton Enright, Tommaso Leonardi, Matthew Davis, Stijn van Dongen
10:30 - 10:45 Tea/Coffee Break
10:45 - 12:00 Introduction to R/BioConductor
12:00 - 13:00 Lunch
13:00 - 14:00 QC, mapping and analysis of a small RNA sequencing dataset Anton Enright, Tommaso Leonardi, Matthew Davis, Stijn van Dongen
14:00 - 15:00 Statistical analysis of a small RNA sequencing dataset
15:00 - 15:15 Tea/Coffee Break
15:15 - 16:30 MicroRNA target analysis using de novo prediction and enrichment based approaches Anton Enright, Tommaso Leonardi, Matthew Davis, Stijn van Dongen
16:30 - 17:00 Questions and Answers, discussion of participants own data and requirements.
Day 2
9:30 – 10:30 Introduction: life after microRNAs Tomás Di Domenico, Konrad Rudolph
10:30 - 10:45 Tea/Coffee Break
10:45 - 12:15 Lecture/Practical: Data Processing part 1 Tomás Di Domenico, Konrad Rudolph
12:15 - 13:15 Lunch
13:15 - 15:00 Lecture/Practical: Data Processing part 2 Tomás Di Domenico, Konrad Rudolph
15:00 - 15:15 Tea/Coffee Break
15:15 - 17:30 Lecture/Practical: Data Analysis Tomás Di Domenico, Konrad Rudolph
Registration Fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, 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

2 days

Frequency

A number of times per year

Related courses
Theme
Specialized Training

Events available