Hi, I would like to know if genomicinteractions package can be used with 4c-seq data. Or which other tools can I use to create a bedpe for further visualization as arc in WUSTL epigenome browser.
Thank you!
Hi there,
Yes, you can use the GenomicInteractions package with 4C-seq data! It is designed to be suitable for any 3D genome interaction method. The makeGenomicInteractionsFromFile function gives some options for importing data, depending on the format of your input file. If your input is not in a format that is supported for direct import, then as a general rule, you will want to provide the constructor function with three things: (1) a GRanges of "anchors" for interactions, in this case your viewpoint region, (2) another GRanges of anchors for interactions, in this case your interacting regions, and (3) a vector of interaction strengths for each pair of GRanges.
Hope that helps and thanks for your interest in the package!
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version 2.3.6
Thank you!
Im a begginer with bioinformatics and genomic data analysis so I will be very grateful If you give me a little help.
I have my interaction data in bedGraph and Wig format which I think are not accepted by the function makeGenomicInteractionsFromFile since this files only have the information corresponding to points (2) (3) that you mention in your answer (interacting regions + counts).
So I think that the second option that you mention is the most suitable for my data, for point (2) I have a GRanges of all the fragments interacting with my viewpoint, for point (1), does the GRanges must be only one line with the viewpoint position? or do I need to make a list with the viewpoint position repeated to generate a list of the same length as (2) GRanges object with all interactions? I also have a list of counts (3) corresponding to al interacting fragments.
Do I need to load this three files as individual objects? or how can I construct an object with the three files in the correct format for further loading in GenomicInteractions?
Thank you very much!
Fernando