This course might be of interest for the members of this list: MANIPULATION OF NGS DATA FOR GENOMIC AND POPULATION GENETICS ANALYSES.
Date: May 14th-17th, 2018, Barcelona (Spain).
PLACE: Capellades, Barcelona.
INSTRUCTORS: Dr. François Sabot (Institute of Research for Development, France) and Dr. Christine Tranchant-Dubreuil (Institute of Research for Development, France)
- Monday, May 14th, 2018.
Introduction to NGS sequencing platforms.
Introduction to basic command lines.
Basic raw data manipulations (counting sequences, listing files).
- Tuesday, May 15th, 2018.
Raw data QC & Cleaning.
Introduction to TOGGLe, a NGS pipeline framework.
Mapping: principle, tools, execution.
Mapping: cleaning, data control, realigning, duplicates marking.
- Wednesday, May 16th, 2018.
SNP calling: raw calling, cleaning calling, filtering.
VCF manipulations: filtering on MAF, heterozygosity…
Impact of SNPs on genes.
Population genomics using sNMF.
- Thursday, May 17th, 2018.
Piping large scale analyses for multiple samples using TOGGLe.
Testing new tools and different conditions to answer different biological questions.
With best regards
Soledad De Esteban-Trivigno,PhD.