Metagenomic: amplicons and stats (03/07/2017 - 06/07/2017)
The Toulouse Genopole bioinformatics platform, Sigenae, NED (GenPhySE) and TWB organize a series of training courses to familiarize yourself with the various resources it provides. These resources are currently: the hardware infrastructure, biological data banks and widely used bioinformatics softwares. This training session, organized by Bioinfo Genotoul, Sigenae, NED (GenPhySE) and TWB, is designed to help you to deal with NGS data of 16S, 18S … DNA produced with MiSeq from Illumina and Roche 454 technologies in the Galaxy workbench. You will discover how to use our Galaxy instance, clean reads, clusterize them, do the taxonomic affiliation and perform statistics to interpret your results.
This training focuses on practice. It consists of four days with a large variety of exercises described hereunder:
- Introduction to Galaxy (Day 1: 09:00 am to 12:30 pm): Galaxy presentation, Upload FROGS data, Use some informatics & bioinformatics tools, How to be a good Galaxy user ?
- FROGS part 1 (Day 1 : 14:00 pm to 17:00 pm): General introduction and objectives, data Upload, introduction to the data: multiplexing / barcoding – illumina/454 – contiged/non-contiged, demultiplexing step
- FROGS part 2 (Day 2 : 09:00 am to 12:30 pm): Pre-processing step: cleaning, clustering step (swarm), clusterStat tool: graphical interpretations, removal chimera step.
- FROGS part 3 (Day 2 : 14:00 pm to 17:00 pm): Filtering step: filters manipulation on the table of abundance, tools for results visualization, Affiliation step: What is RDP/blast ? How to interpret the results in the table of abundance?, brief description of silva database, affiliationStat tool: Graphical interpretations, biomtoTSV tool, Normalisation step.
- FROGS part 4 (Day 3 – 09:00 am to 12:30 pm): Workflow construction, change and analyse the guidelines, conclusion.
- Statistics Analysis with Rstudio part 1 (Day 3 – 14:00 pm to 17:00 pm): general introduction, import and manipulate data, measuring diversity: Alpha, Beta.
- Statistics Analysis with Rstudio part 2 (Day 4 – 09:00 am to 17:00 pm): measuring diversity: Unifrac, Bray Curtis, etc., ordination and dimension reduction: MDS, clustering and heatmap, comparing samples: PERMANOVA, adonis.
The session will take place in the room ‘salle de formation’ at INRA center of Toulouse-Auzeville.