RNASeq – Bioinformatics workshop

RNA-Seq is one of many applications of Next-Generation sequencing. It is basically the sequencing of RNA molecules. RNA-Seq makes it possible to examine the transcriptome, total cellular RNA including mRNA, rRNA and tRNA. Understanding the transcriptome is crucial if we are to properly link information about our genome with its functional expression in the form of protein expression. RNA-Seq can, for example, tell us which genes are turned on in a cell, what their expression level is and at what time they are activated or turned off, all in connection with a certain disease, in response to treatment, under various experimental or environmental conditions etc.

RNA-Seq is a very popular application of NGS, which is inevitably associated with large amount of data and complex procedures for their processing, analysis and interpretation. It is relatively easy to obtain data of this type, but without knowledge of sophisticated procedures on how to handle them, the correct interpretation of the results is very difficult. The situation is also complicated by the rapid development of bioinformatics tools and the fact that there is no generally accepted consensus regarding universally best practice in data processing.

If you are performing an RNA-Seq experiment, it is important that you understand how to access your dataset, how to consider its specifics, and how to track its weaknesses that may limit your ability to draw the right conclusions.

The aim of our workshop is for you to master the bioinformatics procedures of RNA-Seq data processing.


What will you learn?

  • How to select and use the most appropriate procedure for RNA-Seq analysis and how to evaluate its outputs
  • You will become familiar with and use a variety of tools, such as HiSAT2, Salmon, MultiQC, R, DESeq2, FDR, goseq, GO, KEGG ...
  • You will have the opportunity to communicate with an experienced team of speakers and other participants


Who should attend?

  • The event is intended for advanced applicants, biologists or bioinformaticians interested in this specific area of data analysis.
  • Knowledge of BASH and the terminal is a prerequisite. If you have no experience with the analysis of sequencing data, we recommend that you first complete the more general Next-Generation Sequencing data analysis – Workshop for beginners to learn the basics.
  • If in doubt, do not hesitate to contact us.




  • 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




  • The team of lecturers is composed of professionals, employees of SEQme and possibly invited guests - experts on the topic, who have long been using various Next-Generation sequencing technologies. They focus not only on data analysis, but also on laboratory processing of samples in the NGS laboratory, design of NGS projects and other related tasks and are therefore able to provide a comprehensive insight into the whole issue in context.
  • SEQme is not an official distributor of any NGS technology company (Illumina, IonTorrent, PacBio, OxfordNanopore, etc.). We are users, just like you. In our sequencing laboratories, we always use the most suitable technologies from various manufacturers, always with the aim of maximum effect for your sequencing projects. We then share the knowledge gained in this way with the participants of our courses and workshops.


Event details:

  • Trainers always explain the topics using presentations, but the main emphasis is on subsequent practical demonstrations so that all participants actively learn to use the explained procedures and tools
  • All participants themselves perform important steps of NGS data analysis, each has their own computer!
  • We use powerful computers, which are provided to all participants of the event. Using your own computers and / or data files is not possible.
  • If it is an online workshop, you will need your own computer with an Internet connection - you will remotely connect to our powerful analytical computers. There are no special demands on your computer, it is important to have admin rights to install one or two software packages to enable the connection. Simple instructions on how to connect to our workstations will be provided to registered participants well in advance of the event. We recommend that you have headphones to communicate with our lecturers and consider having two monitors - sometimes it is necessary to have multiple windows open at once and having two monitors is comfortable.


Event logistics:

  • Language: English
  • The registration fee includes printed presentations for the course / workshop (for online events, presentations are provided exclusively in electronic form). If this is the „physical“ event (i.e. this is not an online workshop), the price also includes lunches and refreshments.
  • Lodging, travel and other incidental expenses are the responsibility of the attendee.
  • Please note that no laboratory experiments are performed during the event.


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.

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