Live Online Course – 4th Edition
November 11th, 13th, 16th, 18th, and 20th, 2026
This is an introductory course aiming at guiding participants through the execution of the most common pipelines used to analyse different types of transcriptomic data generated through RNA sequencing with NGS technologies.
The course focuses on the use of Linux-based software and tools, although no previous experience with Linux is required.
Places are limited to 16 participants.
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.
RNA-seq
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.
The course is oriented towards graduates or postgraduates with a degree in Biomedical or Life Sciences.
No previous experience working with Linux-based operating systems is required.
All participants must have a personal computer and access to a good internet connection.
Downloading or installing software ahead of the course is not required.
All participants will be given access to a temporary custom-made server with all software and data required for the course. Instructions will be circulated ahead of the course.
Online live sessions on November 11th, 13th, 16th, 18th, and 20th, 2026.
From 14:00 to 18:00 (Madrid time zone).
Total course hours: 26 (20 hours of online live lessons, plus 6 hours of independent work).
This course is equivalent to 1 ECTS (European Credit Transfer System). The recognition of ECTS by other institutions depends on each university or school.
In the live sessions we will combine online lectures with hands-on computational exercises.
Live sessions will be recorded. However, attendance to the live sessions is required to obtain the course certificate.
This course will be delivered in English.
Dr. Marcela Dotto
Instituto de Ciencias Agropecuarias del Litoral
Santa Fé, Argentina
Dr. Hernan G. Rosli
Instituto de Fisiología Vegetal INFIVE
La Plata, Argentina
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