Day 1: Sep 28th

10:30 – 11:00 Registration + coffee

11:00 – 11:30 Course presentation

Francisco García

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

11:30 – 12:00 Introduction to NGS technologies.

Joaquín Panadero

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

12:00 – 13:30 NGS Data Analysis Pipeline

Alejandro Alemán

  • NGS data preprocessing. Handling sequence files. Quality control tools.
  • Mapping. Reference genome as a concept. NGS alignment programs and algorithms. SAM/BAM and BED file formats overview. Mapped reads visualization. Quality control of the mapping. Local realignment. Computational needs.
  • Variant Calling. Variant types: SNPs and InDels. Calling procedures and algorithms. VCF file formats overview. Introduction to the programs GATK, Annovar and Variant. Variant filtering. The problem of the missing data. Variant annotation. Data bases and data repositories: dbSNP, the 1000 Genomes Project and CIBERER Spanish Variant Server.

13:30 – 15:00 Lunch break

Will be held in the cafeteria of the CIPF.

15:00 – 17:30 Prioritization of variants and genes

Francisco García, Francisco Salavert, Alejandro Alemán

  • Introduction to genome browsers. Presentation.
  • BiERapp. Interactive web application for assisting in gene prioritization in Whole-Exome Sequencing studies.
  • CSVS (CIBERER Spanish Variant Server). This database provides information about the variability of the Spanish population. It is very useful for filtering polymorphisms and local variations when prioritizing candidate disease genes.

Day 2: Sep 29th

9:30 – 11:00 Panel of Genes

Mercedes Medina

11:00 – 11:30 Coffee break

11:30 – 13:30 RNA-Seq Data Analysis from Babelomics 5

Marta Hidalgo, Matías Marín

13:30 – 15:00 Lunch break

Will be held in the cafeteria of the CIPF.

15:00 – 16:30 Functional Profiling: FatiGO and Gene Set Analysis

16:30 – 17:30 Practical session

Alejandro Alemán, Francisco Salavert, Asunción Gallego, Mercedes Medina, Francisco García

  • NGS data preprocessing, mapping and variant calling.
  • Working with all analysis webtools. Bring your data!

21:00 Social dinner

  • Asador Pipol. C/ Convento San Francisco, 3. Maps

Day 3: Sep 30th

9:30 – 11:00 Functional Profiling: Network Analysis

José Carbonell

Functional profiling and detection of new functional candidates:

11:00 – 11:30 Coffee break

11:30 – 13:30 Pathways Analysis

Cankut Çubuk, Alicia Amadoz, Marta Hidalgo, José Carbonell

13:30 – 14:00 Closing

Joaquín Dopazo

14:00 – 15:30 Lunch

Will be held in the cafeteria of the CIPF.

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.