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

October 23rd - 24th 2014

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


  • 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


To be announced...


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).

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)


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).


ecSeq Bioinformatics
04275 Leipzig


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