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.
Key Dates
- Opening Date of Registration: April 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)
Registration fees:
- industry rate: 850 EUR
- academic rate: 600 EUR
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
Register
When you register for this workshop you are agreeing with our [Workshop Terms and Conditions][5]. Please read them before you register.
[5]: http://www.ecseq.com/workshops/workshop_TermsAndConditions.html
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