Hands-On Training in Discovering Standard and Non-standard Transcripts

ecSeq Bioinformatics · 04-27-2014, 04:06 AM

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: events@ecSeq.com

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.

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04-27-2014, 04:06 AM	#1
ecSeq Bioinformatics Senior Member Location: Leipzig, Germany Join Date: May 2012 Posts: 271	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: events@ecSeq.com 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. sponsored by media partner Find more information at http://www.ecseq.com/workshops/workshop_2014-04.html __________________ ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS). Last edited by ecSeq Bioinformatics; 07-15-2014 at 06:28 AM.

07-15-2014, 06:31 AM	#2
ecSeq Bioinformatics Senior Member Location: Leipzig, Germany Join Date: May 2012 Posts: 271	I am very excited to announce that Pacific Biosciences decided to sponsor this course and send a speaker to give a short presentation, highlighting the benefits of ultra-long reads in isoform detection. __________________ ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).