RNAseq alignment, quantification and transcripts discovery

RNAseq alignment, quantification and transcripts discovery (17/10/2019 - 18/10/2019)

The Toulouse Genotoul bioinformatics platform, in collaboration with the MIAT unit, organize a 1,5 day long training course for bio-informaticians and biologists aiming at learning sequence analysis. It focuses on (protein coding) gene expression analysis using reads produced by ‘RNA-Seq’. This training session is designed to introduce sequences from ‘NGS’ (Next Generation Sequencing), particularly Illumina platforms (HiSeq). You will discover the standards file formats, learn about the usual biases of this type of data and run different kinds of analyses, such as spliced alignment on a reference genome, novel gene and transcript discovery, expression quantification of coding genes and transcripts. The biostatistics part (differential expression analysis) is NOT included.



This training focuses on practice. It consists of modules with a large variety of exercises described hereunder:

  • Introduction: What will be my experimental plan? What is gene expression? What kind of technology can be used to monitor gene expression? What do the reads produced by NGS platforms (Illumina) using the RNA-Seq protocol look like? Which are the known biases of these sequences? Presentation of the dataset for the practical exercises.

  • Sequence quality and Sequence cleaning.

  • Splice aligning reads on a reference genome.

  • Visualizing alignments and splice sites using IGV (Integrated Genome Viewer).

  • Raw count vs. abundance estimate.

  • Discovering novel genes and transcripts.

  • Comparison of models, visualization and results of gene expression quantification and conclusions.


The session will take place in the room ‘salle de formation’ at the INRA center of Toulouse-Auzeville.


Prerequisites: ability to use a Unix and Cluster environment (see Unix training and Cluster). Training materials will be available on the website before the session. Slides will be downloadable from our web site. A Unix reference command leaflet will also be provided. Only the latter will be available during the session.



Bookings: RNAseq alignment, quantification and transcripts discovery

This event is fully booked.