3DAROC21

3C-based data analysis and 3D reconstruction of chromatin folding

Course Timetable

The times displayed refer to the time zone of Lisboa, PT

Mon,
Oct 4th
Day #1
10:00 - 10:15 Welcome and introduction [PDF]
10:15 - 10:45 Overview on structure determination [PDF]
10:45 - 11:00 Break
11:00 - 11:30 Overview of 3D genomes [PDF]
11:30 - 12:00 Break
12:00 - 13:00 Live Introduction to Linux and working environment [PDF]
13:00 - 16:30 Videos
Introduction to TADbit and data handling for 3C-based experiments (12 minutes) [see video] [PDF]
From raw data to Hi-C contact matrices (14 minutes) [see video] [PDF]

Notebooks
01-Inspect_Hi-C_input_data.ipynb
02-Generate_mapper_index.ipynb
03-Hi-C_Quality_Check.ipynb
04-Mapping.ipynb
05-Parsing.ipynb
16:30 - 17:30 Live Discussion
Tue,
Oct 5th
Day #2
10:00 - 10:30 Live Discussion
10:30 - 11:00 Chromatin structure and 3C data [PDF]
11:00 - 12:00 Integrative modeling applied to chromatin with TADbit [PDF]
12:00 - 17:00 Videos
Hi-C contact matrices: filtering (17 minutes) [see video] [PDF]
Biological applications I: TAD response to hormone treatment) (26 minutes) [see video] [PDF]
Biological applications II: SOX2 gene activation dynamics) (26 minutes) [see video] [PDF]

Notebooks
06-Intersecting_and_Filtering_mapped_reads.ipynb
07-Bin_filtering_and_normalization.ipynb
08a-Compartments_detection.ipynb
17:00 - 18:00 Live Discussion
Wed,
Oct 6th
Day #3
10:00 - 10:30 Live Discussion
10:30 - 17:00 Videos
Comparison between experiments (10 minutes) [see video] [PDF]
Biological applications: III: IMGR, combining image and Hi-C data for modeling) (24 minutes) [see video] [PDF]

Notebooks
08b-TADs_detection.ipynb
09-Compare_and_merge_Hi-C_experiments.ipynb
09b_CHESS_Compare_chromatin_contact_data.ipynb
10-Modeling_parameters_optimization.ipynb
11-3D_Models_production_and_analysis.ipynb
12-3D_Modeling_molecular_dynamics_TADdyn.ipynb
17:00 - 17:30 Live Discussion and farewell
Course Homepage

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated: October 4th 2021