Skip to content
Jim Robinson edited this page Feb 4, 2019 · 9 revisions

Other viewers:

Data:

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

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:

Noisy data

The data is noisy, and there are occasional crazy outliers. What to do about it?

  • Have option to right-click and remove a sphere. The structure would then be broken there (same as a NAN)
  • Automatically remove spheres > certain distance from their neighbors. We know the genomic distance between centroids, so we can estimate with good accuracy the maximum possible physical distance. The distance between base pairs in a double helix is ~ 3.4 Angstroms (0.34 nanometers). So in a 30kb window the centroids cannot be more than ~10,000 nm.