Hands-On Training in Discovering Standard and Non-standard 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.
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 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.
Contact
ecSeq Bioinformatics
Brandvorwerkstr.43
04275 Leipzig
Germany
Email: [email protected]
Downloads
Download flyer
Register
When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.
When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.
sponsored by
media partner
Find more information at http://www.ecseq.com/workshops/workshop_2014-04.html
Comment