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dozmorovlab / TADCompare

Package for analysis and characterization of differential TADs
https://dozmorovlab.github.io/TADCompare/
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Suggestion for analysis - dealing with replicates #13

Closed TerezaClarence closed 1 year ago

TerezaClarence commented 2 years ago

Dear TADCompare developers,

I would like to ask for your opinion; I am dealing with large HiC dataset and I have multiple replicates for for each celltype (and timepoint). Is it possible to generate Consensus TADs on each cell type (from several replicates) and then run pairwise TADCompare on ConsensusTAD_celltype1 vs ConsensusTAD_celltype2 objects?

Also, is it possible to do the same thing for TimeCompare? Compare consensusTAD objects for multiple timepoints rather that have a single Hi-C data for each time point? (Again, I have multiple replicates for each timepoint).

Thank you for your suggestions!

Best, Tereza

mdozmorov commented 2 years ago

It is possible to call consensus TADs and prespecify them for TADcompare. The only problem is that TADcompare requires a pair of Hi-C matrices and it is unclear which ones to use. For time-course, no, it works with one matrix per time point.

These are great case scenarios we need to work on.