Attention! - Workshop venue has changed
Dear participants, please kindly notice that we had to change the workshop venue. The workshop will take place at Hotel Prokop Square, Prokopovo nám. 472/10, Prague. The hotel not only offers its meeting rooms for our workshop but you can use it during your stay in Prague at a discounted rate (12% off). Please contact us in case of interest.
Some people think RNASeq data analysis is easy. They are wrong!
RNASeq, sometimes also known as whole transcriptome sequencing, is the sequencing of a sample's mRNA content. Notably, it is a method by which a point-in-time snapshot of the transcriptome can be obtained.
Easy it sounds, difficult it gets! This is why we organize this workshop every year and 2024 is no exception. You will be introduced into the Linux operating system and than you will do ... RNASeq data analysis! By using various free tools.
Join our 9th edition of the in-person RNASeq workshop in 2024 and experience true enthusiasm!
Day 1 - As simple as it gets
- 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 and 3 - NGS data handling
- 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 and 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
Who Should Attend?
- Biologists, bioinformaticians, healthcare professionals and laboratory workers interested in analyzing RNASeq data
- Great for beginners
- Suitable also if you want to deepen or revive your knowledge
What will you learn?
- Well, you will learn RNASeq Data Analysis ... :-) Basic handling of raw reads and read mapping, selecting the most appropriate RNASeq analysis approach etc.
- You will gain hands-on experience using a range of data resources and tools: HiSAT2, Salmon, MultiQC, R, DESeq2, FDR, goseq, GO, KEGG...
Prerequisites
- This is a hands-on computer workshop with presentations and practical demonstrations.
- A necessary prerequisite is computer literacy and basic knowledge of molecular biology (DNA, RNA, gene expression, PCR). Knowledge of BASH and the terminal is not required but is an advantage.
General information
- Language: English
- Printed presentations are provided for in-person events, pdfs for online events (will be emailed to you a few days before the online event commences).
- For in-person events lunches and refreshments are included.
- All tools we use during our events are open-source (free). We never use licenced software unless explicitely stated.
- All participants of our hands-on workshops perform important steps of data analysis themselves, each has their own computer we provide. Using your own computers and / or data files during our data analysis workshops is not possible.
- Time is always CET.
- Lodging, travel, and other incidental expenses (if applicable) are the responsibility of attendees.
- No laboratory experiments are conducted during our events.
- For all our events you will receive a certificate of completion.
About us
This event is organised by SEQme company. We are an NGS-service provider with laboratories located in the Czech Republic and serving several hundreds of clients every year.
We organize courses and workshops since 2012. Our team of speakers is comprised of our employees, NGS lab specialists, data analysts and bioinformaticians. For selected events from our portfolio we work together also with our external partners and collaborators, usually bioinformaticians with deep knowledge of particular application-specific pipelines.
Head of our Courses & Workshops programme: Stepan Stoces
Please send your inquiries to ngs@seqme.eu
We can make it a turnkey event for your team only. Do not hesitate to contact us!
