Discovering standard and non-standard RNA transcripts
How to detect canonical splicing, circular RNAs, trans-splicing, and fusion transcripts


When?
October 23rd - 24th 2014

Where?
Leipzig, Germany

Scope and Topics

The purpose of this workshop is to get a deeper understanding in the usage of split-read mapping in order to find splice junctions, predict new isoforms and uncover non-standard RNA molecules, like circularized RNAs or fusion-transcripts. Advantages and disadvantages of the so-called split-reads and their implications on data analyses will be covered. The participants will be trained to understand the mapping approach, to find potential problems/errors and finally to implement their own pipelines. After this course they will be able to find and analyze (non-)standard exon-exon junctions and create ready-to-use analyses pipelines. In the course we will use a real-life RNA-seq dataset from the current market leader illumina.

By the end of this workshop the participants will:

  • understand the implications of splicing or fusion events and the concept of split-reads
  • understand how to detect splice sites using split-read information
  • know how to predict and quantify different isoforms of genes
  • be able to find circularized RNAs or fusion-stranscripts
  • be able to perform differential splicing analyis
  • automate tasks with shell scripting to create reusable data pipelines
  • plot and visualize results
  • be able to reuse all analyses

Requirements

  • basic linux knowledge (shell usage, common commands). You should be familiar with the commands covered in the Learning the Shell Tutorial
  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)
  • knowledge in standard HTS analyses and data formats (FASTQ, SAM, samtools, ...)

Target Audience

  • biologists or data analysts with some experience in analyzing HTS data

Included in Course

  • Course materials
  • Catering
  • Conference Dinner

Program

To be announced...

Speakers

Gero Doose (University of Leipzig) found and published several circularized RNAs in various RNA-Seq experiments. He specialized on split-read analysis some years ago and has a strong expertise in downstream analyses.

Christian Otto (University of Leipzig) is one of the developers of the split-read mapping tool segemehl and is an expert on implementing efficient algorithms for HTS data analyses.

David Langenberger (ecSeq Bioinformatics) started working with small non-coding RNAs in 2006. Since 2009 he specialized on NGS technolgies. He has been part of several large NGS projects, for example the International Cancer Genome Consortium (ICGC).

Guest-speaker:
Invited speaker (Pacific Biosciences) will give a short presentation about the benefits of ultra-long reads in isoform detection.

Key Dates

Opening Date of Registration: April 1st 2014
Closing Date of Early Registration: May 1st 2014
Closing Date of Registration: August 1st 2014
Workshop: October 23rd-24th 2014 (8:00 - 17:00)

Attendance

Location: Leipzig, Germany.
Language: English
Available seats: 20 (first-come, first-served)

Travel expenses and accommodation are not covered by the registration fee.

Note: Combine this workshop with our other workshops and get 10% discount (this discount does not apply to early registrations).

Contact

ecSeq Bioinformatics
Brandvorwerkstr.43
04275 Leipzig
Germany
Email: events@ecSeq.com

Downloads

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