Question: extracting scaffoldnames from HiC contact matrix
0
gravatar for m.t.lorenc
9 weeks ago by
m.t.lorenc0
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 ?

Thank you in advance,

Mic

hic • 120 views
ADD COMMENTlink modified 8 weeks ago by bioparticles.melly0 • written 9 weeks ago by m.t.lorenc0
Answer: extracting scaffoldnames from HiC contact matrix
0
gravatar for Aaron Lun
9 weeks ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

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

ADD COMMENTlink written 9 weeks ago by Aaron Lun23k

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

ADD REPLYlink written 9 weeks ago by m.t.lorenc0

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.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Aaron Lun23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 378 users visited in the last hour