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  • 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

    October 23rd - 24th 2014

    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

    • 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


    To be announced...


    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).

    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)


    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.


    ecSeq Bioinformatics
    04275 Leipzig
    Email: [email protected]


    Download flyer

    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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    Last edited by ecSeq Bioinformatics; 07-15-2014, 05:28 AM.
    ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).

  • #2
    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).


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