News: Bioinformatics Hands-On Workshop: Discovering standard and non-standard RNA transcripts

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-transcripts
be able to perform differential splicing analysis
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.