TAD boundaries

[hansenp]

For Mifsud 2015, I found table Suppl Table 2 TAD. It seems that this table contains non overlapping TAD regions for CD34 and GM12878. Here two lines of one of these tables:

chr1    3960001 6080000
chr1    6080001 8040000

I wonder, if this could be converted to a file like this:

chr1    6080000 6080001
chr1    8040000 8040001

This could be imported to GOPHER in order to set all digest that overlap a boundary active.

[hansenp]

For Nora 2017, I found table S6. But I'm not sure how to interpret the content. It's also about compartments...

[hansenp]

Header of table S6:

TABLE LEGEND - REFER TO METHODS FOR STATISTICAL DETAILS |  
-- | --
  | log2_insulation_score_100kb: see methods. Note that local minima identify bins with the greatest insulation potential (see methods)
  | log2_insulation_score_100kb_dip_prominence: the relative amplitude of the local minima of the insulation score with respect to adjacent local maxima. The threshold we set to call boundaries is 0.3 (see methods). Higher dip prominence indicate more locally insulating boundaries
  | n_bad_bins: number of filtered 20kb-bins within 100kb. For our analysis we only retained boundaries with 0 or 1 filtered bins to avoid artificial boundaries produced by low-coverage bins
  | compartment-transition: one of neighbouring bins has a different compartment assignment
  | cis_eigenvector_20kb: eigenvector value for the bin
  | compartment: assignment of the bin to the A- or B- compartment
  | untreated_boundary: bin called as boundary in untreated CTCF-AID cells
  | gone_boundary: bin called as boundary in untreated but not in after 2 days of auxin in CTCF-AID cells
  | residual_boundary: bin called as boundary 2 days of auxin in CTCF-AID cells, which was also had a boundary in the untreated sample within +/- 1 bin
  | residual_CTCFless_boundary: bin called as boundary 2 days of auxin in CTCF-AID cells, which was also had a boundary in the untreated sample within +/- 1 bin, removing bins that had a CTCF ChIP-seq peak after 2 days of auxin within +/-1 bin
  | neighboring CTCF / Pol2 / H3K36me3: bin has a ChIP-seq peak for corresponding feature within +/- 1 bin
  | neighboring compartment transition: transition from A/B compartment within +/- 1 bin

Maybe we could use these two columns:

  | untreated_boundary: bin called as boundary in untreated CTCF-AID cells
  | gone_boundary: bin called as boundary in untreated but not in after 2 days of auxin in CTCF-AID cells