The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course 3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding are open. with Marc Marti-Renom, François Serra and Davide Baù IMPORTANT DATES for this Course Deadline for applications: September 30th 2016 Notification of acceptance within 72 hours of application (working days count) Course date: Oct 10th to Oct 14th 2016 Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/3DAROC16 for details. Course Description 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in the space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php ; http://promoter.bx.psu.edu/hi-c/view.php or http://www.aidenlab.org/data.html ). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: 1D - Map paired-end sequences to generate Hi-C interaction matrices 2D - Normalize matrices and identify constitutive domains (TADs, compartments) 3D - Generate populations of structures which satisfy the Hi-C interaction matrices 4D - Analyze and compare different samples. Participants can bring- specific biological questions and/or their own 3C-based data to analyse during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyse Hi-C data. Note: Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB@igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb