• Advanced Courses in Life Sciences

    Header of Genetics and Genomics at Transmitting Science

Live Online Course – 2nd Edition

Introduction to RNA-seq bioinformatic pipelines

October 15th-23rd, 2024

Live sessions will be recorded

Course Overview & Programme

This is an introductory course aiming at guiding students through the execution of the most common pipelines used to analyze different types of data generated through RNA sequencing with NGS technologies.

The course focuses on the use of Linux-based software and tools and is oriented to graduates or postgraduates with a degree in Biomedical or Life Sciences. No previous experience working with Linux-based operating systems is required.

Brief introduction to Linux
Linux OS. Using the terminal, commands and utilities to operate on files and directories. Examples to operate on fasta and fastq files.

Quality control and pre-processing of fastq files
Fastq format. FastQC package and fastx_toolkit for pre-processing fastq files.

SAM format and samtools
Overview of bioinformatic pipelines for RNA sequencing data. Samtools package to operate and extract information from sam files.

Overview and step-by-step pipeline. Description of input files and ribosomal RNA filtering. Mapping to reference genome. Transcript assembly and quantification. Differential expression analysis and downstream analysis.

Small RNA sequencing
Special considerations for small RNA sequencing. Mapping to reference genome. Classification according to size. Example of a pipeline for differential expression analysis. Tools for miRNA target prediction.

LncRNA discovery
Characteristics of long non-coding RNA (lncRNA). Step-by-step pipeline for lncRNA discovery.

All participants must have a personal computer and access to a good internet connection.

For the purposes of the course, participants’ machines should have at least 100 Gb free space on their hard drive, and as much RAM as possible.


Marcela Dotto instrutor for Transmitting Science

Dr. Marcela Dotto
Instituto de Ciencias Agropecuarias del Litoral
Santa Fé, Argentina

Hernan Rosli instructor for Transmitting Science

Dr. Hernan G. Rosli
Instituto de Fisiología Vegetal INFIVE
La Plata, Argentina

Dates & Schedule

Online live sessions on 15th ,16th, 18th, 21st, and 23rd of October

From 13:00 to 17:00 (Madrid time zone)

Total course hours: 26 

20 hours of live sessions, plus 6 hours of participants working on their own.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.



This course will be delivered live online

The course will be taught using a combination of live (synchronous) sessions on Zoom and Slack.
Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.


Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end.

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno
Transmitting Science

Haris Saslis instructor for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Fees & Discounts

  • Course Fee
  • Early bird (until August 31st, 2024):
  • 496 €
    (396.80 € for Ambassador Institutions)
  • Regular (after August 31st, 2024):
  • 610 €
    (488 € for Ambassador Institutions)
  • Prices include VAT.
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration.

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.


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