visualization of 3C interactions

bogdan · 01-25-2012, 08:27 AM

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 · 01-26-2012, 12:29 AM

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 · 01-26-2012, 03:22 PM

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

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01-25-2012, 08:27 AM	#1
bogdan Member Location: san diego Join Date: Jul 2008 Posts: 35	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? thanks, Bogdan

01-26-2012, 03:22 PM	#3
bogdan Member Location: san diego Join Date: Jul 2008 Posts: 35	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

01-26-2012, 12:29 AM	#2
simonandrews 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.