• Learn the essential computing skills for NGS bioinformatics
  • Understand NGS analysis algorithms (e.g. read alignment) and data formats
  • Use bioinformatics tools for handling NGS data
  • Perform first downstream analyses for studying genetic variation
  • Compare different approaches for differential expression analysis


Overview

The purpose of this intense one week summer course is to get a deep understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. You will be trained on understanding NGS data formats and handling potential problems/errors therein. In the summer school we will use a real-life RNA-seq dataset from the current market leader illumina.

All students will be enabled to perform important first tasks of NGS data analysis themselves. The layout of the summer school has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and fast evolving research topic.

In the evenings there will be social events, like a conference dinner, or a guided city tour through Berlin. These are always great networking possibilities.

Read our detailed course program.

Agenda

  1. Linux for Bioinformatics:
    This module will introduce the essential tools and file formats required for NGS data analysis. It helps to overcome the first hurdles when entering this (for NGS analyses) unavoidable operating system.
  2. Introduction to NGS data analysis:
    Different methods of NGS will be explained, the most important notations be given and first analyses be performed. This course covers essential knowledge for analysing data of many different NGS applications.
  3. RNA-seq Data Analyses: In this module different bioinformatics tools for RNA-seq alignment will be described and tested. We then apply and compare the various approaches for differential expression analysis using RNA-Seq.
  4. DNA Variant Calling: In this module different bioinformatics strategies for variant calling will be described. We then predict our own variants and jointly interpret and discuss several examples.

Detailed Course Program


Linux for Bioinformatics

  • Introduction to the command line and important commands
  • Combining commands by piping and redirection
  • Introduction to bioinformatics file formats and databases (e.g. UCSC, ENSEMBL)
  • Usage of important bioinformatics toolkits

Introduction to NGS data analysis

  • Introduction to sequencing technologies from a data analysts view
  • Raw sequence files (FASTQ format)
  • Preprocessing of raw reads: quality control (FastQC), adapter clipping, quality trimming
  • Introduction to read mapping (Alignment methods, Mapping heuristics)
  • Read mapping (BWA, BWA-MEM, Bowtie2, STAR, segemehl)
  • Mapping output (SAM/BAM format)
  • Usage of important NGS toolkits (samtools, BEDtools)
  • Mapping statistics
  • Visualization of mapped reads (IGV, UCSC)

RNA-seq Data Analyses

  • Understand split-read mapping
  • Run different split-read mappers (tophat, STAR)
  • Run pseudo-alignment tool salmon
  • Understand the Tuxedo Suite (cufflinks, cuffcompare, cuffmerge, cuffdiff, etc.)
  • Understand the statistics behind DEseq2 and DIEGO
  • Quantify exons/genes/transcripts
  • Predict
    • Differential splicing using DIEGO
    • Differential gene expression using DEseq2
    • Differential isoform expression using cuffdiff
  • Create extensive diagnostic graphics with R
  • Apply your new skills by working on challenging exercises
NOTE: We will NOT cover single-cell RNA-Seq

Analysis of genetic variation

  • DNA variant calling: methods and tools
  • Variant Call File Format (VCF)
  • Filtering and annotation of genetic variants

Speakers

Invited Speakers (short talks)

University
Prof. Dr. Katja Nowick Free University of Berlin

Research Facility
Dr. Michael Jahn Max Planck Unit for the Science of Pathogens


Your summer school trainers

Dr. Gero Doose (ecSeq Bioinformatics GmbH)
Gero 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. Publications

Dr. Adam Nunn (ecSeq Bioinformatics GmbH)
Adam is an expert bioinformatician skilled in developing data analysis pipelines. He specializes in whole genome DNA-Seq, de-novo genome assemblies, bulk RNA-Seq, and single-cell RNA-Seq. Adam's expertise enables him to extract valuable insights from complex datasets, unraveling gene expression patterns. Publications

Dr. David Langenberger (ecSeq Bioinformatics GmbH)
David started working with small non-coding RNAs in 2006. Since 2009 he uses NGS technologies to investigate these short regulatory RNAs as well as other targets. He has been part of several large NGS projects, for example the International Cancer Genome Consortium (ICGC). Publications



Requirements

The target audience is biologists or data analysts with no or little experience in analyzing NGS data. A fundamental understanding of molecular biology (DNA, RNA, gene expression, PCR, ...) is assumed.

Included in the Summer School

  •   Course materials
  •   Catering during the workshop
  •   High-performance workstations (no laptop needed)
  •   Conference Dinner
  •   Guided city tour
  •   Networking opportunities
  •   Certificate

Attendance

Location: PC-College, Stresemannstraße 78, 10963 Berlin, Germany
Language: English
Available seats: 30 (first-come, first-served)

Registration Fee: 1,549 EUR (excluding VAT)

Travel expenses and accommodation are not covered by the registration fee.

Travel Information - Berlin

Key dates

Opening Date of Registration: December 13, 2023
Closing Date of Registration: May 31, 2024
Workshop: June 10-14, 2024 (9 am - 5 pm)

What our participants are saying

"Excellently structured and polished workshop! The material was challenging but the way it was presented made it easy to follow and fun to engage with. The tutors made the learning environment really friendly and safe, and I got much more out of this workshop than I initially expected. Thank you!" Antonina Karakostova, University of Copenhagen, Denmark

"The course provided an excellent introduction to the analysis of NGS data and covered the most relevant aspects in a well-structured and comprehensible way. The trainers did a really great job guiding us step-by-step through the NGS data analysis workflow and providing theoretical background information and lots of hands-on experience. Overall, a very informative and well-organised course - clear recommendation!" Thomas Wulff, Max Planck Unit for the Science of Pathogens, Germany

The course was dense, well paced, but no stone was left unturned, particularly for statistics and "black boxes", which I particularly enjoyed. Organisation was very good, as well. The wit and expertise of the instructors made this the best such course I have so far attended." Alex Tomazatos, Bernhard Nocht Institute for Tropical Medicine, Germany


When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please review them before you register.





Any Questions? Please feel free to contact our events team.

ecSeq Bioinformatics GmbH
Sternwartenstr. 29
D-04103 Leipzig
Germany
Email: events@ecSeq.com