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

[Peter Cock]

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
>
>
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