Notes

Data:

• https://github.com/BogdanBintu/ChromatinImaging
• http://sgt.cnag.cat/3dg/datasets/files/20180717_Nir_etal_2018_Dataset.zip

Other viewers:

• https://bsiranosian.shinyapps.io/shiny_structure_explore/
• http://3dgenomes.github.io/TADkit/#!/project/browser?conf=assets%2Fexamples%2Fconf.json
• http://delta.big.ac.cn/
• http://csynth.org/

Online viewer for the Nir et al models (pdb).

• http://jenalib.leibniz-fli.de/cgi-bin/3d_mapping.pl?CODE=

_Note: Data is in "data/Nir/Models". The Nir PDB model files are broken, there is no space between the x&y coordinates. These are easy to fix, find the position which needs a space and use sed. For example, file CS1A.pdb was fixed as follows

sed 's/.\{38\}/& /' CS1A.pdb

IGV session for IMR-90 CTCF and RAD21 tracks:

• http://bit.ly/2t4iDrA