New feature request of Virtual-4C map if possible?

[Zhibo M.]

Would it be possible to add a tool that could use the juicer output data to create virtual-4C map?

Wash U 3D genome browser supports the virtual-4C viewing using hic data, but it has to be in BUTLER format.

HiC-Pro included a utility python script to make a bedgraph file from its mapped hic output file.

The result from juicer is more consistent with our previous 3C data on some high resolution loops. So I prefer using juicer.

I want to make a virtual-4C map based on viewPoint range of selection.

I am pretty new in linux and bioinformatics and not sure how to do it right. I am thinking the observed reads could be extracted using the mapped_nondup_sorted as input and extract lines that one end is in the set viewPoint range. But I am not sure how to deal with the expected value, could they be simply merged into a larger bin (set viewpoint range here)?

Anyone could help?

And if possible, I am wondering if Neva or your colleges could develop a new feature that could allow people to view virtual4C result from the juicer HiC output. The idea is somewhat similar to Capture-HiC. The final output does not needs to be juicerbox format, bedgraph format would be enough.

Thanks,

Zhibo

[Muhammad Saad Shamim]

Hey Zhibo,

This feature is available already with juicer/juicebox. Open up your hic file in juicebox and go to the location/resolution/normalization you'd like. The right click and select generate 1D horizontal/vertical track. It will be created as a wig file.

I'll upload some picture instructions when I'm back on my laptop.

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[Zhibo M.]

Thanks for the instructions. And I found the generate 1D track function via right click.

I found that this feature/function is only available for observed reads. When I select observed/expected, right click won't give the options to generate 1D track.

And would it be possible to also allow us to set a range as viewPoint/anchor for the 1D track generation?

If these additional functions are not available from the current juicerbox, do you have any suggestions on how to make a virtual 4C-like 1D track based on a range as viewPoint? And if possible, also on observed/expected values?

Thanks,

Zhibo

[Samuel Kaplan]

Hi Zhibo,

I am also looking to create virtual 4C tracks with ranges as the view points. Did you find a way of doing this?

Also, have you come across alternatives to the right-click method of generating the virtual 4C tracks from ".hic" files? Looking for a way to do it through code, if possible.

Thanks,

Sam

[Berkley Gryder]

I'm also looking for the same solution (making a genome-wide wig or bedgraph from a single coordinate slice for virtual 4C).  Any answer yet?  Can STRAW or DUMP be used for this?