sRNAseq

sRNAseq (16/08/2016)

The GenoToul bioinformatics platform, Sigenae, NED (GenPhySE) and TWB , organize a series of training courses for bio-informaticians and biologists aiming at introduce analysis of sequences produced by next-generation sequencers. An initial training on sequence alignment and polymorphisms search is provided in this context, since mid-2010. In 2011, a second course has been produced on protein coding gene expression analysis using reads produced by ‘RNA-Seq’. In the present session, we introduce small RNA-seq data analysis and focus on miRNA detection, annotation and differential expression. This training session is designed to help you to deal with small RNA sequences produced from the NGS (Next Generation Sequencing) technology particularly Illumina platforms (HiSeq). You will discover sequence file formats, learn about expression profiles of miRNA and other small non coding RNA and run different kinds of analyses such as reads cleaning, alignment on a reference genome, detection and annotation of new and known miRNA, and expression quantification.

 

This training is focused on practice. It consists of 3 modules with a large variety of exercises:

• Introduction (09:00 am to 10:30 am): what are non coding RNA ? What are the characteristics of miRNA genes and miRNA expression? What kind of technology can be used to monitor gene expression? What do the reads produced by NGS platforms such as Illumina Solexa using the sRNA-Seq protocol look like? Which are the known biases of these sequences ?
• Controlling the reads quality and data cleaning. (10:45 am to 12:30 pm)
• Prediction and expression (14:00 pm to 17:00 pm): miRNA alignment against a reference genome. Annotation of known and novel miRNA. Quantifying miRNA expression. Differential expression.

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

Prerequisites: ability to use a Unix environment (see Unix training). Training materials will be available on the website before the session. Slides in a “taking notes” format 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: sRNAseq