RNA-Seq Data Analysis Workshop
Quality Control, Read Mapping, Visualization and Downstream Analyses

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Advance your research. Understand RNA-Seq analyses challenges and solve them yourself.

In a nutshell

  • Learn the essential computing skills for NGS bioinformatics
  • Understand NGS analysis algorithms (e.g. read alignment) and data formats
  • Use bioinformatics tools for handling RNA-Seq data
  • Create diagnostic graphics and statistics
  • Compare different approaches for differential expression analysis

When?
March 11 - 14, 2024

Where?
Berlin, Germany

46 votes

Scope and Topics

The purpose of this workshop is to get a deeper 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 course we will use a real-life RNA-seq dataset from the current market leader illumina.

All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout 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.

Read our detailed course program.

Our Philosophy

Get trained by experts

Our trainers have a proven record of academic and/or industrial experience in NGS data analysis. Because up-to-date expert knowledge is needed to answer your questions and know what is important in the field.

Open source NGS tools

We only use open source tools that are free to use. We try to showcase and compare different tools (e.g. NGS mappers), since not every software fits with every task/question.

Learn effectively with well-curated materials

For a optimal learning experience we carefully prepare our learning materials and example data. All materials, tools and results created during the course are for take home with you.

Workshop Design

This workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics and comprises this three course modules:

  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 module covers essential knowledge for analysing RNA-Seq data.
  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 bulk RNA-Seq.
NOTE: We will NOT cover single-cell RNA-Seq data analysis in this course.

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)

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)
  • Understand split-read mapping
  • Run different split-read mappers (tophat, STAR)
  • Run pseudo-alignment tool salmon
  • Mapping output (SAM/BAM format)
  • Usage of important NGS toolkits (samtools)
  • Mapping statistics
  • Visualization of mapped reads (IGV, UCSC)

RNA-seq Data Analyses

  • 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

Speakers

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. 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

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. 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 Course

  •   Course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance workstations (no laptop needed)
  •   Certificate

Attendance

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

Registration Fee: 1,449 EUR (excluding VAT)

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

Travel Information - Berlin

Key dates

Opening Date of Registration: October 16, 2023
Closing Date of Registration: March 1, 2024
Workshop: March 11 - 14, 2024 (9 am - 5 pm)

What our participants are saying

"Great experience, helpful and approachable instructors, interesting and well organized workshop. This course provided necessary training in NGS that can be used in research projects. Personally, being in the early stages of my undergraduate studies in Molecular Biology and Genetics this workshop really inspired me and expanded my horizons. More specifically, by meeting participants from all around the world who are involved in various fields of science, attending talks from external guest speakers who described their career path and getting to know the instructors of the course who were full of enthusiasm about Bioinformatics, I realized the interconnection between the scientific fields and the different professional options that I could potentially be involved with in the future." Ioanna Gkogka, Molecular Biology and Genetics Democritus University of Thrace, Greece

"The course was designed for people starting their work with RNA-Seq and was very well prepared and led. The information is provided in a clear and accessible manner and, most importantly, from a practical point of view. The trainers have extensive experience and provide valuable insights into the real problems arising from data analysis. I am happy to have had opportunity to attend these workshops. The knowledge and skills acquired during the workshops will be of great help in planning my own experiments and will enable me to start analyze the data on my own. I definately recommend these workshops to anyone planning RNA-seq experiments." Dorota Magner, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poland

"I was particularly impressed with the emphasis on teaching us how to THINK about our analyses, rather than just follow a series of commands. Your focus on anticipating potential sources of error, never blindly trusting that a command or piece of software has done what you think it's done without confirming (as well as teaching us ways to confirm) left us with a skill set that is independent of a particular pipeline, and will serve us well as our interests (and the available software) change. The active exercises were clearly designed extraordinarily carefully and were really effective not just in applying what we'd just learned, but in seeing how you might fall into an analysis/interpretation trap if you are not careful. This really was a mindset/philosophy of analysis training as much as it was practical training, and I value that enormously. Thank you!" Morgan Benowitz-Fredericks, Bucknell University, USA

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