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Whole transcriptome data analysis – Course and Conference Office

EMBL Course

Whole transcriptome data analysis

Overview

Course overview

This course will teach the biological researchers how to analyse biological data sets using open-source software. Most of the analysis will be performed with docker4seq and rCASC packages, which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis. Docker4seq and rCASC packages use docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers. This approach provides multiple advantages: the user does not need to install all the software on its local server, the results generated by different containers can be organised in pipelines and reproducible research is guarantee by the possibility of sharing the docker images used for the analysis.

Computers for hands-on exercises will be provided along with demo data sets.

Audience

This course was developed for biological researchers as the intended audience. Basic knowledge of massively parallel sequencing (MPS) is desirable, however R-coding skills and deep knowledge of statistics are not necessary.

Modules/Resources

  • Tools for RNA-seq and single cell RNA-seq data analysis
  • Experimental design (RNAseq/scRNAseq)
  • Quality control (RNAseq/scRNAseq)
  • Normalisation and data reformatting (RNAseq/scRNAseq)
  • Basic statistics (RNAseq)
  • Selecting differentially regulated genes/microRNAs (RNAseq)
  • Multiple testing (RNAseq)
    • Dimensionality reduction (scRNAseq)
    • Clustering (RNAseq/scRNAseq)
  • Biological interpretation (RNAseq/scRNAseq)

Learning outcomes

  • Understand the importance of experimental design in order to ask sensible biological questions
  • Assess the quality of your data
  • Perform normalisation and reformatting procedures
  • Complete basic statistical tests on Next Generation Sequencing (NGS) data
  • Understand some of the problems encountered when analysing data

What past participants say about this course

“My research focus is on RNA sequencing, infectious diseases and next generation sequencing. Attending this course helped me understand the basics, got me career advice and extended my network. Overall, it made me a better researcher.” – Abhay Deep Pandey, Translational Health Science And Technology Institute, India

“Excellent course on the complete spectrum of RNA-Seq. I would highly recommend this course to all biologists.” – Issaac Rajan, King Abdullah University of Science and Technology, Saudi Arabia

Speakers

Speakers, trainers, and staff

Scientific organisers

Course organisers

Programme

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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
  • All times in the programme below are shown as the time in Europe/Berlin.
  • The preliminary programme is a draft and is subject to change.
Day 1 – Sunday 21 May 2023
Time (Berlin/Europe)SpeakerLocation
13:30EMBL shuttle bus from ISG to EMBLISG Hotel entrance
14:00-14:30Arrival, welcome, course overview and safety briefing
Vladimir Benes – EMBL Heidelberg, Germany
Inna Bösselmann – EMBL Heidelberg, Germany
Irena Provaznikova – EMBL Heidelberg, Germany
Courtyard Room A&B
14:30-15:00Participants flash talksCourtyard Room A&B
15:00-16:00RNA-seq, cool but is it that simple?
Vladimir Benes – EMBL Heidelberg, Germany
Courtyard Room A&B
16:00-16:30Coffee BreakCourtyard Foyer
16:30-18:00RNA-seq, cool but is it that simple?
Vladimir Benes – EMBL Heidelberg, Germany
Courtyard Room A&B
18:00-19:00DinnerEMBL Canteen
19:00EMBL shuttle bus to ISG HotelATC Entrance
Day 2 – Monday 22 May 2023
Time (Berlin/Europe)SpeakerLocation
08:40Embl shuttle bus from ISG to EMBLISG Hotel entrance
09:00-10:00R pills theory and practice
Marco Beccuti – University of Turin, Italy
Computer Training Lab
10:00-10:30Coffee BreakATC Foyer
10:30-11:00Experimental design
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
11:00-12:00Docker4seq/rCASC/4SeqGUI overview
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
12:00-13:00LunchEMBL Canteen
13:00-13:30Docker container and reproducibility
Marco Beccuti – University of Turin, Italy
Computer Training Lab
13:30-14:30QC bulk
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
14:30-15:00Coffee BreakATC Foyer
15:00-16:00QC single cells
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
16:00-17:30R pills theory and practice
Marco Beccuti – University of Turin, Italy
Computer Training Lab
17:30 – 18:30Social programme: Facility tour
18:30-20:10DinnerEMBL Canteen
20:15EMBL shuttle bus to ISG HotelATC Entrance
Day 3 – Tuesday 23 May 2023
Time (Berlin/Europe)SpeakerLocation
08:40EMBL shuttle bus from ISG to EMBLISG Hotel entrance
09:00-10:30R pills theory and practice
Marco Beccuti – University of Turin, Italy
Computer Training Lab
10:30-11:00Coffee BreakATC Foyer
11:00-12:30Counting reads and data reduction
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
12:30-13:30LunchEMBL Canteen
13:30-15:00Counting reads and data reduction
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
15:00-16:00Counting reads miRNA
Francesca Cordero – University of Turin, Italy
Computer Training Lab
16:00-16:30Coffee BreakATC Foyer
16:30-18:00ExercisesComputer Training Lab
18:00-19:00R pills theory and practice
Marco Beccuti – University of Turin, Italy
Computer Training Lab
19:00-20:30DinnerEMBL Canteen
20:30EMBL shuttle bus to ISG HotelATC Entrance
Day 4 – Wednesday 24 May 2023
Time (Berlin/Europe)SpeakerLocation
08:40Hoffmann Bus from ISG to EMBLISG Hotel entrance
09:00-10:00Differential expression analysis for bulk RNAseq
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
10:00-11:00Sub-population discovery in single cell RNAseq: clustering
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
11:00-11:30Coffee BreakATC Foyer
11:30-12:30Differential expression analysis for multiple groups: ANOVA-like
Raffaele Calogero – University of Turin
Computer Training Lab
12:30-13:30Lunch and group photoEMBL Canteen
13:30-15:00Exercises Bulk RNAseqComputer Training Lab
15:00-16:00Exercises single cell RNAseqComputer Training Lab
16:00-16:30Coffee BreakATC Foyer
16:30-18:00R pills theory and practice
Marco Beccuti – University of Turin, Italy
Computer Training Lab
18:00EMBL shuttle bus to restaurantATC Entrance
19:00Social Dinner at Oskar Restaurant
Day 5 – Thursday 25 May 2023
Time (Berlin/Europe)SpeakerLocation
08:40Hoffmann Bus from ISG to EMBLISG Hotel entrance
09:00-10:00R pills theory and practice
Marco Beccuti – University of Turin, Italy
Computer Training Lab
10:00-11:00Mining differential expression results for bulk RNAseq
Raffaele Calogero – University of Turin, Italy
Computer Training Lab
11:00-11:30Coffee BreakATC Foyer
11:30-12:30Depicting clusters specific biomarkers in single cell RNAseq data
Francesca Cordero – University of Turin, Italy
Computer Training Lab
12:30-13:30Lunch EMBL Canteen
13:30-16:00ExercisesComputer Training Lab
16:00-16:30Coffee BreakATC Foyer
16:30-17:30ExercisesComputer Training Lab
17:30-18:30R pills theory and practice
Marco Beccuti – University of Turin, Italy
Computer Training Lab
18:30-20:00DinnerEMBL Canteen
20:00EMBL shuttle bus to ISG HotelATC Entrance
Day 6 – Friday 26 May 2023
Time
(Berlin/Europe)
SpeakerLocation
08:40EMBL shuttle bus from ISG to EMBLISG Hotel entrance
09:00-11:00 Individual exercises on bulk or single cell RNAseq
Raffaele Calogero – University of Turin, Italy
Marco Beccuti – University of Turin, Italy
Computer Training Lab
11:00-11:30Coffee BreakATC Foyer
11:30-12:30Individual exercises on bulk or single cell RNAseq
Raffaele Calogero – University of Turin, Italy
Marco Beccuti – University of Turin, Italy
Computer Training Lab
12:30-13:30LunchEMBL Canteen
13:30-16:00Individual exercises on bulk or single cell RNAseq
Raffaele Calogero – University of Turin, Italy
Marco Beccuti – University of Turin, Italy
Computer Training Lab
16:00-16:20Final remarks
Vladimir Benes, Raffaele Calogero, Marco Beccuti
Computer Training Lab
16:30Hoffmann shuttle bus to Heidelberg Train StationATC Entrance

Practical information

Registration fees and motivation letter

The course is limited to 28 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration Fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks.

Participants are expected to book and pay their own accommodation and travel expenses. 

Academia€690
PhD Student€690
Industry€1200

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For more detailed information, follow the instructions provided in our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles

Single rooms have been reserved for 6 nights (20 – 26 May 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code DAT23-01). We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Technical requirements and event software

Technical requirements

Below you will find the software and technical requirements for this course.

  • All software and hardware required for this course will be ready for you to use in our Computer Training Lab.
  • You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
  • If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
  • Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Additional Information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for onsite events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 21 - 26 May 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:

  • Marco Beccuti
    UNIVERSITY OF TURIN, ITALY

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