Table of Contents

GENOMIC VARIATION COURSE

Day 1

9:00 – 9:30 Registration

9:30 – 10:00 Course presentation

Joaquín Dopazo

  • General overview of the course.
  • NGS technologies, analysis methods and webtools.

10:00 – 11:00 Introduction to NGS technologies for Genomic Analysis

Joaquín Panadero

  • Basics of the NGS technologies.
  • Computing infrastructure for NGS analyses.
  • Some remarks on experiment design.

11:00 – 11:30 Coffee break

11:30 – 12:00 Introduction to Linux

Francisco Salavert Presentation

12:00 – 13:00 Quality Control for Raw Data

13:00 – 14:30 Lunch break

Will be held in the cafeteria of the CIPF.

14:30 – 16:00 Mapping NGS Reads and Visualization for Genomic Studies

Joaquín Tárraga

16:00 – 16:30 Coffee break

16:30 – 18:00 Variant Calling SNPs and INDELs. Variant Annotations

José Carbonell


Day 2

9:30 – 11:00 Biological and Clinical Databases

11:00 – 11:30 Coffee break

11:30 – 13:00 Prioritization of variants and genes: BiERapp (I)

13:00 – 14:30 Lunch break

Will be held in the cafeteria of the CIPF.

14:30 – 16:00 Prioritization of variants and genes: BiERapp (II)

Francisco García

16:00 – 16:30 Coffee break

16:30 – 18:00 Bring your own data!

Alejandro Alemán, Francisco García, Francisco Salavert, Joaquín Tárraga, José Carbonell, Alicia Amadoz

  • During this session you can analyze your data with us.
  • You can also do the exercises of other sessions.
  • If you do not have any data, this will not be a problem and here we have a full practice for you: http://bioinfo.cipf.es/gda16/doku.php/ngstutorial.

21:00 Social dinner


Day 3

9:30 – 11:00 Panel of Genes: Design and Analysis for Clinical Applications. TEAM (I)

11:00 – 11:30 Coffee break

11:30 – 12:30 Panel of Genes: Design and Analysis for Clinical Applications. TEAM (II)

Alejandro Alemán

12:30 – 13:00 Closing

13:00 – 14:30 Lunch break

Will be held in the cafeteria of the CIPF




TRANSCRIPTOMICS COURSE

Day 1

14:30 – 15:00 Course presentation

Francisco García

15:00 – 16:00 Introduction to NGS technologies for Expression Analysis

Joaquín Panadero

16:00 – 16:30 Coffee break

16:30 – 18:00 Primary Analysis for RNA-Seq Data: Quality Control, Mapping and Quantification

Joaquín Tárraga


Day 2

9:30 – 11:00 Normalization & Differential Expression Analysis

11:00 – 11:30 Coffee break

11:30 – 13:00 Clustering and Supervised Classification Analysis

13:00 – 14:30 Lunch break

Will be held in the cafeteria of the CIPF.

14:30 – 16:00 Functional Profiling from Babelomics 5: FatiGO and Gene Set Analysis

16:00 – 16:30 Coffee break

16:30 – 18:00 Functional Profiling from Babelomics 5: Network Analysis

Cesim Merten

21:00 Social dinner


Day 3

9:30 – 11:00 Signaling Pathways Analysis: hiPathia

Cankut Çubuk, Marta R. Hidalgo

11:00 – 11:30 Coffee break

11:30 – 12:30 Signaling Pathways Analysis: PathAct

José Carbonell, Alicia Amadoz

Exercise

PathAct Exercise

gene expression data from GSE57156

12:30 – 13:00 Brunch

Will be held in the cafeteria of the CIPF.

13:00 – 15:00 Mascletà

15:00 – 15:30 Coffee break

15:30 – 16:30 Enrichment Analysis for microRNAs

Francisco García

16:30 – 17:30 Bring your own data!

Joaquín Tárraga, Marta Hidalgo, Daniel Crespo, Cesim Merten, Cankut Çubuk, Alicia Amadoz, José Carbonell, Francisco García

17:30 – 18:00 Closing



References and links

  • Babelomics 5.0: functional interpretation for new generations of genomic data. Alonso R, Salavert F, Garcia-Garcia F, et al. Nucleic Acids Res. 2015;43:W117-W121.
  • Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. Hernansaiz-Ballesteros RD, Salavert F, Sebastián-León P, Alemán A, Medina I, Dopazo J. Nucleic Acids Res. 2015;43:W270-W275.
  • Understanding disease mechanisms with models of signaling pathway activities. Sebastian-Leon P, Vidal E, Minguez P, et al. BMC Syst Biol. 2014;8(1):121.
  • Inferring the functional effect of gene expression changes in signaling pathways. Sebastián-León P, Carbonell J, Salavert F, Sanchez R, Medina I, Dopazo J. Nucleic Acids Res. 2013;41:W213-W217.
  • A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W88-W93.
  • A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Alemán A, Garcia-Garcia F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W83-W87.
  • SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J. Nucl. Acids Res. 2009;37:W109-114
  • Genome Maps, a new generation genome browser. Medina I, Salavert F, Sanchez R, et al. Nucleic Acids Res. 2013;41:W41-W46.