NSCPHD1212 UCSC genome browser analyses

Volume 2014/2015
Content
  • Overall course description

The UCSC Genome Browser is an on-line genome browser that is physically hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. Through a strategic collaboration between UCPH and UCSC we here offer a unique opportunity for UCPH PhD students to explore the full power of the UCSC Genome Browser at a hands-on Genome Browser training at UCSC.

  • This course will be held at UC Santa Cruz, US in week 33 (10-14 August)

 

  • Subject area

Exploring RNA Biology using bioinformatics and UCSC Genome Browser tools for analysis and visualization.

  • Scientific content

Introduction to the UCSC Genome Browser (Sofie Salama, UCSC)

The UCSC Genome Browser is a powerful tool for displaying multidimensional information and annotations mapped to specific genomic coordinates. This session will expose students to other tools available through the Genome Browser interface, including querying the annotation databases using the UCSC Table Browser.

RNA-Seq data and mapping (Professor Anders Krogh, KU)

This session will introduce and compare the programs for mapping of sequencing reads as well as methods for transcriptome assembly.

RNA-Seq based expression profiling (Professor Jakob Skou Pedersen, AU and Angela Brooks, UCSC)

This session will introduce and compare several widely used software packages for RNA-seq data. Critical parameters including quality control (QC) as well as the strengths and limitations of different programs application will be discussed.

Methods for RNA folding (Professor Paul Gardner, University of Christ Church, NZ and Professor Jakob Skou Pedersen, AU)

The students will be introduced to and apply different methods for predicting RNA structure.

Analysis of ncRNA and ncRNA databases (Professor Paul Gardner, University of Christ Church, NZ)

In this session students will explore the theoretical and technical aspects of ncRNA discovery, including RNA structure homology searches. The students will discuss the limitations and strengths of existing computational tools for ncRNA discovery.          

RNA modifications (Professor Todd Lowe, UCSC)

In this session the students will learn about RNA modification and new high throughput methods for detection of these.

Introduction to genomic analysis of protein-nucleic acid interactions (Associate Professor Jeremy Sanford, UCSC)

This session will explore the technical, theoretical and practical aspects of methods for interrogating protein-RNA and protein-DNA interactions. A focus will be placed on CLIP-Seq, RIP-Seq, CHIP-seq, HiC and 4C.

tRNAs (Professor Todd Lowe, UCSC)

Students will learn about tRNA transcription, structure-based function prediction, and new roles for tRNA fragments.

Analysis of ncRNA and ncRNA databases (Professor Paul Gardner, University of Christ Church)

In this session students will explore the theoretical and technical aspects of ncRNA discovery. The students will discuss the limitations and strengths of existing computational tools for ncRNA discovery.

Introduction to miRNA and RNA motif analysis (Professor Anders Krogh, KU and Associate Professor Jeppe Vinther, KU)

Students will learn about methods for finding RNA motifs, including miRNA binding motifs.

Introduction to global analysis of RNA Structure (Associate Professor Jeppe Vinther, KU)

In this session students will learn about experimental methods for probing RNA structure in gene and how these methods can be applied on a global scale.

Analysis of high throughput RNA structure data sets (Professor Jakob Skou Pedersen, AU)

In this session students will learn about algorithms for predicting secondary and tertiary RNA structures based on genomic sequences and from chemical probing experiments. Technical considerations including data QC, comparative genomics, and RNA-folding landscapes will be discussed.

One day symposium

In addition there will be one day with invited speakers from Denmark and the Bay area and a poster session, where student can bring their own poster and discuss their data with the teachers and other participants.

 

Learning Outcome
  • Students will be able to create data structures that are compatible with specific analysis tools.
  • Students will be able to apply different state-of-the-art analysis tools depending on the experimental design of the high throughput assay.
  • Students will understand the ethics of genomic data analysis and be able to archive high throughput datasets and analysis pipelines prior to publication.
This course is aimed at the biologist who is interested in exploring protein-coding genes using the University of California Santa Cruz (UCSC) Genome Browser. It is geared towards those who have little or no experience using theUCSC Genome Browser and for more advanced users who are not familiar with many of the gene-oriented browser features
MSc in molecular biology, biology, bioinformatics, biomedicine or similar background.
Lectures, tutorials, hands-on training session, group exercises
  • Category
  • Hours
  • Class Instruction
  • 20
  • Practical exercises
  • 20
  • Preparation
  • 20
  • Project work
  • 40
  • Total
  • 100
Credit
4 ECTS
Type of assessment
Course participation