7th Prague Autumn School - RNASeq Data Analysis Workshop

10 October 2022 09:00 - 14 October 2022 17:00, Prague, Czech Republic

After several successful years we are again inviting you to join our data analysis workshop which covers all basic steps of Next-Generation sequencing data analysis.
This five day computationally-intensive workshop focuses on quality control, sequence editing, read mapping and alignment. Additionally, this year we will pay a special attention to RNASeq data analysis.

You will be briefly introduced into the Linux operating system and in this environment you will analyze sequencing data using various publicly available tools.

Who should attend?
This workshop is aimed at beginners as well as advanced users, life scientists and bioinformaticians interested in the analysis of Next-Generation sequencing data. No prior knowledge of sequences data analysis or specific programming skills are required.

What will you learn?
  • How to perform basic manipulations with raw sequences and read mapping
  • How to choose and accomplish the most appropriate approach to RNASeq and evaluate its outcome
  • You will gain hands-on experience using a range of data resources and tools
  • You will have the option of networking with experienced team of speakers and other participants
And what will you get?
  • At the last day of the week you will be provided with a bootable USB stick with all tools used and data analyzed
  • All your 5-day work stored and ready to be used immediately when you get back to your lab!
During the workshop…
  • Trainers will provide lectures with follow-up hands-on exercises in order to have the participants learning and assessing their knowledge
  • All workshop participants will perform all data analysis tasks themselves!
  • The powerful computer infrastructure available at the conference center will be used (no personal laptops are required/allowed)
  • Overall, get ready for a very intensive week…

Workshop agenda
Day 1: Linux as a scientific tool - Go beyond the graphical interface
  • General introduction to data analysis
  • Unix environment for bioinformatical analysis
  • Introduction to the Linux system
  • Basic commands in Terminal and their practical use
  • Overview of common data formats
Day 2-3: Basic operations with NGS data - Get the full picture of NGS workflow
  • Working with data from NCBI and other databases (SRAtool kit)
  • Quality control of sequence data (FastQC, MultiQC, ...)
  • Editing sequences in various programs (FASTX-toolkit ...)
  • Introduction to alignment
  • Alignment and read mapping
  • Introduction to R
Day 4-5: RNASeq data analysis
  • Mapping to genome and gene expression estimation
  • Mapping to transcriptome and transcript abundance estimation
  • Count data standardization and quality control
  • Exploratory data analysis, dimensionality reduction, clustering
  • Analysis of differential expression
  • Multiple comparisons problem
  • Biological interpretation using Gene Set Enrichment Analysis
  • Data visualization
Various tools will be explained and used including but not limited to HiSAT2, Salmon, MultiQC, R, DESeq2, FDR, goseq, GO, KEGG...

Our team of speakers includes professionals focusing on data analysis but also sample processing in Next-Generation Sequencing lab and other related tasks and therefore as a team able to provide a comprehensive insight into the whole data analysis workflow in context.
  • David Dufour Rausell, Bioinformatician, SEQme
  • Michal Kolář, Bioinformatician, Institute of Molecular Genetics
  • Jiří Novotný, Bioinformatician, Institute of Molecular Genetics
  • Štěpán Stočes, Bioinformatician, SEQme
Workshop Logistics
  • Language: English
  • Registration fee includes: Workshop materials, Lunches/Coffee breaks
  • Please kindly notice that lodging, travel and other incidental expenses are the responsibility of the attendee and that no labwork is to be performed during the workshop
A basic knowledge of BASH, Unix terminal and R usage are not necessary but advantageous. If you are a newbie to the field, we recommend you go through some tutorials.

Special offer: All our courses and workshops can also be organized at your workplace, for your working group. So as a tailor-made event. Some of our events were even created in this way - at the client's request. The advantage of this format is, of course, the ability to prepare a turnkey event for your team, reflect your specific requirements and needs, including the ability to work with your data. If you are interested, do not hesitate to contact us.
Conference Centre, Institute of Molecular Genetics

Conference Centre, Institute of Molecular Genetics, Videnska 1083, Prague, 14220, Czech Republic

Organised by
SEQme, Dlouha 176, Dobris, 26301 Czech Republic.
We pride ourselves on providing full solutions in the field of DNA sequencing.
Workshops and courses since 2012.
Contact information
Richard Nadvornik
SEQme s.r.o.
Contact us by email

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