visualizing genomic data

[bogdan]

Dear all,

I would appreciate if you can recommend any software package where I can display a set of features/annotations (eg genes, TF binding sites), and intra- or inter-chromosomal 3C interactions data (as lines between interaction loci, or just simply as dots that count for an interaction strength at a particular position). thanks,

bogdan

[simonandrews]

If you have the interaction data already then you can use something like circos to visualise this.

If you only have raw mapped paired datasets (HiC type experiments) then the choice of user-friendly software to handle these is pretty limited. We introduced some HiC support in the last release of SeqMonk and there will be greatly expanded support in the next release (due out very soon now). We'd be keen to hear from any groups working on this kind of data who might be interested in trying the tools out.

[bogdan]

Thanks for suggestions. As in Hi-C, we do have paired data of the loci that interact. Now the question would be if I can transform these numbers that account for interaction pairs into a different graphical format: eg lines, dots, etc ... let's say:

in one track, I do represent the interactions between A and B1, B2, ..., Bn loci.
in another track, I do represent interactions between X, and Y1, Y2, ....Yn loci.

thanks !