Question: extracting scaffoldnames from HiC contact matrix
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5 months ago by
m.t.lorenc0 wrote:

Hello, I ran 3d-dna and loaded the results into JuiceBox ( ).

The screenshot ( https://imgur.com/a/izTbb54 ) shows the loaded results. Scaffolds and their names are in green boxes within the chromosomes bins (blue boxes). I am interested to extract the scaffold names for each chromosome.

Is there a way to extract scaffold names (green box ) inside each blue box as shown with any tool ?

Mic

hic • 162 views
modified 5 months ago by bioparticles.melly0 • written 5 months ago by m.t.lorenc0
Answer: extracting scaffoldnames from HiC contact matrix
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5 months ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

Neither 3D-DNA or JuiceBox are Bioconductor packages. You'd be better off asking the authors directly.

Does Bioconductor have any packages which are able to read hic files and get this way the scaffold names?

Not that I know of, but I haven't kept up to date with the latest packages for Hi-C data analysis. I just had a look at the hic format specification on https://github.com/aidenlab/Juicebox, and this was not particularly informative with respect to how one could read it from another framework. It would be nice if they based their format on something like HDF5, but I guess they don't intend for other people to poke their noses into their files. That's fair enough; defining a format properly is hard work.