visualization of 3C interactions

[bogdan]

Dear all,

please could you recommend any package (apart from CIRCOS) where the interchromosomal interactions (by 3C method - chromatin conformation capture) could be visualized?

thanks,

Bogdan

[simonandrews]

We've recently added a load of new functions to SeqMonk to handle this type of data. It can represent HiC/ChiAPET data as a heatmap, or can create 4C type datasets from any arbitrary positions which can then be quantitated and plotted on a genome-wide view in the same way as a normal 2D dataset.

This is still an area of active development, so more suggestions for how to handle or represent this type of data are very welcome.

[bogdan]

3C interactions

Dear Simon,

thanks for the note. Yes, I have been thinking about SeqMonk a while ago :
we could of course interact offline on any potential software developments that may be useful for 3C community ..

Bogdan