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LAST CALL: Discovering Cancer-Specific 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:
Find more information at http://www.ecseq.com/workshops/workshop_2014-04.html
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
Find more information at http://www.ecseq.com/workshops/workshop_2014-04.html