[Biopython] HiC - extracting scaffold names from a contact matrix

[Mic]

Hi Peter,
Sorry, that I posted here. My questions relates to Bioinformatics and I
thought maybe there is a Python library around.

The screenshoot shows scaffolds and their names (green boxes) within the
chromosomes bins (blue boxes). I am interested to extract the scaffold
names for each chromosomes so I could compare the two results from ALLHiC
and 3d-dna for each chromosomes.

Thank you in advance,

Mic

On Fri, 11 Jan 2019 at 19:52, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Hello Mic,
>
> I don't understand you question and how it relates to Biopython.
> Do you mean starting from the output of  3d-dna and/or ALLHiC,
> how to match scaffold names to the diagonal entries (green boxes)?
>
> Peter
>
> On Fri, Jan 11, 2019 at 4:02 AM Mic <mictadlo at gmail.com> wrote:
> >
> > Hello,
> > I ran 3d-dna and ALLHiC. Both of them showing in JuiceBox (
> https://www.youtube.com/watch?v=Nj7RhQZHM18 ) different chromosome size
> bins (blue). Is there a way to extract scaffold names (green box ) inside
> each blue box as shown here ( https://imgur.com/a/izTbb54 ) ?
> >
> > Thank you in advance
> >
> > Mic
> >
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
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