Hands-on High throughput Sequencing course in Bogota with the collaboration of Institut Pasteur and UniAndes

Hands-on course on High Throughput Sequencing data analysis: Genomics, Transcriptomics, Epigenomics

About

The University of Los Andes and the Hub of Bioinformatics and Biostatistics of the C3BI (Center of Bioinformatics Biostatistics and Integrative Biology) at Institut Pasteur will organize this Hands-on course aimed at students/researchers that have produced HTS data sets and would like to learn how to get the most out of it. This course will provide a general introduction to the bioinformatic and statistical aspects of HTS data analysis, alternating theory and practice. The objective is to present the general concepts such as file formats, mapping of sequences, as well as, the specific procedures for each data type: DNA-Seq, RNA-Seq, ChIP-Seq. An additional session will be devoted to the pathway and functional analysis for gene set issued from differential or other kind of analysis.
Knowledge of the basic Linux and R commands is highly recommended.
Please be aware that the workshop will be delivered both in Spanish and English.

Trainers

Programme

   
 
  • 08:00 – 8:30 Registration
  • 08:30 – 12:30
    • Presentation of the course
    • Introduction to HTS/NGS technologies (Illumina, PacBio, NanoPore, etc.) [T]
    • Basic stats/probability concepts: particularities of HTS/NGS sampling, underlying distributions, etc. [T]
  • 14:00 – 18:00
    • Quality analysis (error and bias of different technologies, quality metrics in sequencing, etc) [T/P]
    • Introduction to file formats (FASTA, FASTQ, SAM, BAM, BED, GFF …) [T/P]
 
  • 08:30 – 12:30
    • Alignment and mapping algorithms [T]
    • Mapping against a reference – Mapping for removal of contaminants [P]
  • 14:00 – 18:00
    • Assembly [T/P]
 
  • 08:30 – 12:30
    • Transcriptomics: Expression quantification, differential analysis, splice variant analysis [T/P]
  • 14:00 – 18:00
    • Epigenomics [T/P]: Quality control of IP enrichment, peak calling and introduction to differential analysis [T/P]
 
  • 08:30 – 12:30
    • Pathway analysis and functional analysis [T/P]
  • 14:00 – 18:00
    • Introduction to analysis in Galaxy
    • Visualization of data sets in the genome browser IGV
 

Registration

Registration is compulsory. Please proceed to the following link to complete your registration.

Location

Universidad de los Andes
Bogotá, Colombia
Carrera 1 #18A-12
https://uniandes.edu.co/en   Enregistrer

Inception – 2017 doctoral allocations



The Inception (INstitut Convergence : Emergence of Pathology Through Individuals and PopulatiONs) program, supported by the call Institut Convergence des Investissements d’Avenir, is launching a call for the recruitment of PhD students in transversal and interdisciplinary projects aimed at understanding the emergence of pathologies through individuals and populations.  
  • Search profiles

The selection of projects will be made in two stages and will be based on the following criteria :
• quality and interdisciplinary nature of the project
• scientific excellence of supervisors and host teams
• academic excellence of the student (good basic knowledge in biology, interest in life sciences and medical applications, solid training in the following fields : mathematics, statistics, computer science, physics, social sciences)
 
  • Application and eligibility

The selected projects will fall within the main subjects of the Inception program and will have to meet the following criteria:
• Interdisciplinary project on the emergence of pathologies, associating biology, medicine, mathematics, statistics, computer science, physics, social sciences …
• the cross-cutting nature must be clearly demonstrated and its added value to answer the questions addressed in the project.
• co-supervision between two teams belonging to complementary fields of competence
• at least one of the project teams must be affiliated with the Institut Pasteur (Paris); The other team (s) must be affiliated to one of the Inception partners (Institut Pasteur included, see website).
 
  • Two-stage procedure

1) the research teams must fill out a single pdf document (INCEPTION Template Call PhD 2018) and send it before October 16, 2017 using the form on this page (https://c3bi.pasteur.fr/careers/inception-2018-phd-application/)

the document will include:
• the summary of the file (1 page)
• detailed project (max 4 pages)
• the CVs of the supervisors and presentations of their laboratories (1 page each)

Selected projects will be announced in December 2017.

2) the candidate for the allocation must send a single pdf document by April 01, 2018 (Link and template to come) including :
• the student CV (1 page) and a letter of motivation (1 page)
• notes and rankings of M1 and M2
• the opinion of the doctoral school to which the candidate will report for his/her thesis.
Except in special cases, discuss in advance, the candidates will be auditioned by the jury of the doctoral school Frontières du Vivant, partner of the Inception program.

Results will be released after this auditions (Beginning of July 2018).
 
  • Dates of the call

• Open date (teams): September 01, 2017
• Closing: October 16, 2017
• Selection by Inception Steering Committee: November 2017
• Open date (students): February 01, 2018
• Closing: April 01, 2018
• Selection by Inception Steering Committee and auditions: June 2018
• Funding start: October 2018
  • Contact

INCEPTION_PHD2018@pasteur.fr

Available position for research unit in bioinformatics with the C3BI