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Old 01-25-2012, 08:27 AM   #1
Location: san diego

Join Date: Jul 2008
Posts: 35
Default visualization of 3C interactions

Dear all,

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


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Old 01-26-2012, 12:29 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

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.
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Old 01-26-2012, 03:22 PM   #3
Location: san diego

Join Date: Jul 2008
Posts: 35
Default 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 ..

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