.hic to full matrix

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dozt...@gmail.com

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Jun 4, 2018, 11:12:21 PM6/4/18
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Hello everybody,

I have a pre-analyzed .hic data and I would like to convert it to full matrix. Is there any way that I can do this? I know the Straw and dump commands, but these are not creating a full matrix per se.

Thank you very much.

Best Regards,

Dogancan

Moshe Olshansky

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Jun 5, 2018, 3:00:02 AM6/5/18
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Hi Dogancan,

dump -d creates full matrix. 

dozt...@gmail.com

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Jun 5, 2018, 11:47:08 AM6/5/18
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Hi,

What I mean by full matrix is that I want all the interactions in one matrix with a specific bin size. However, dump asks me to provide the chromosome number.

Dogancan

5 Haziran 2018 Salı 00:00:02 UTC-7 tarihinde Moshe Olshansky yazdı:

Neva Durand

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Jun 5, 2018, 11:48:09 AM6/5/18
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You will need to dump all chromosome-chromosome combinations.

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Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab

dozt...@gmail.com

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Jun 5, 2018, 11:52:07 AM6/5/18
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What about interchromosomal interactions?

Dogancan

5 Haziran 2018 Salı 08:48:09 UTC-7 tarihinde Neva Durand yazdı:
You will need to dump all chromosome-chromosome combinations.
On Tue, Jun 5, 2018 at 11:47 AM, <dozt...@gmail.com> wrote:
Hi,

What I mean by full matrix is that I want all the interactions in one matrix with a specific bin size. However, dump asks me to provide the chromosome number.

Dogancan

5 Haziran 2018 Salı 00:00:02 UTC-7 tarihinde Moshe Olshansky yazdı:
Hi Dogancan,

dump -d creates full matrix. 

On Tuesday, June 5, 2018 at 1:12:21 PM UTC+10, dozt...@gmail.com wrote:
Hello everybody,

I have a pre-analyzed .hic data and I would like to convert it to full matrix. Is there any way that I can do this? I know the Straw and dump commands, but these are not creating a full matrix per se.

Thank you very much.

Best Regards,

Dogancan

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To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.

Neva Durand

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Jun 5, 2018, 11:57:44 AM6/5/18
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Send in the chromosomes, i.e. "1 3"

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dozt...@gmail.com

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Jun 5, 2018, 2:49:08 PM6/5/18
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Yes sure, but how to combine all of them into one full matrix? (either coordinated-list or tab-seperated matrix)?

5 Haziran 2018 Salı 08:57:44 UTC-7 tarihinde Neva Durand yazdı:

Neva Durand

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Jun 5, 2018, 3:02:25 PM6/5/18
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You will have to write your own custom script.  If you're not worried about big files you can dump dense matrices, then you would combine them in a double for loop.  Otherwise you can dump sparse matrices, which will save space, and then put in the zeros as needed.

What is the application for which you need a giant dense matrix?

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dozt...@gmail.com

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Jun 5, 2018, 3:24:03 PM6/5/18
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I think there is a need for that. There are couple of visualization tools that requires full matrix as well some other loop callers.

Thank you very much for the answers!

Dogancan



5 Haziran 2018 Salı 12:02:25 UTC-7 tarihinde Neva Durand yazdı:

Neva Durand

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Jun 5, 2018, 3:35:19 PM6/5/18
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I do encourage you to look at our visualization tools (Juicebox and Juicebox.js, aidenlab.org/juicebox ) as well as HiCCUPS.  

Dense matrices, especially genome-wide, are not practical for the resolutions at which one can explore loops (5K and higher), at least not for mammalian genomes.

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dozt...@gmail.com

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Jun 5, 2018, 3:59:05 PM6/5/18
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Thanks! I'll check it out.

Dogancan

5 Haziran 2018 Salı 12:35:19 UTC-7 tarihinde Neva Durand yazdı:
I do encourage you to look at our visualization tools (Juicebox and Juicebox.js, aidenlab.org/juciebox ) as well as HiCCUPS.  

dozt...@gmail.com

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Jun 6, 2018, 1:37:06 PM6/6/18
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I want ask one more question. Can you produce kind of .bedpe file from the .hic formatted data?

Thanks,

Dogancan

5 Haziran 2018 Salı 12:59:05 UTC-7 tarihinde dozt...@gmail.com yazdı:

Neva Durand

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Jun 6, 2018, 4:47:49 PM6/6/18
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No; the data is binned and no longer at bp resolution.  We have tools for manipulating the data in hic files.


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