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

[Peter Cock]

Hi Mic,

I would start by examining any data files these tools output (not just
their graphical output).

You might also have more success with a Q&A site like
https://www.biostars.org/ - but if you do post a question there or on
StackExchange or similar, I would urge you to include a link to this
discussion to avoid duplication of effort:

https://mailman.open-bio.org/pipermail/biopython/2019-January/016587.html

Thanks,

Peter

On Sat, Jan 12, 2019 at 9:36 PM Mic <mictadlo at gmail.com> wrote:
>
> 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
>> >
>> >
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