3D Genomics

1–30 of 1417

Welcome to the Aiden Lab's Forum for all questions, comments, and concerns relating to 3D Genomics, including the Hi-C protocol, Juicebox visualization software, and Juicer pipeline!

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YN HAO, Neva Durand5

Sep 17

No data can be extract from .hic file whether normalized or not

Hi Neva, Thanks for your help and so powerful tool. When we converted the valid pairs to hicfile, no

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No data can be extract from .hic file whether normalized or not

Hi Neva, Thanks for your help and so powerful tool. When we converted the valid pairs to hicfile, no

Sep 17

Nayden Chakarov, … Nayden Chakarov3

Sep 17

vertebrate sex chromosomes

Hi Olga, I did assemblies of two bird species but have problems interpreting the PAR region of one of

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vertebrate sex chromosomes

Hi Olga, I did assemblies of two bird species but have problems interpreting the PAR region of one of

Sep 17

Giovanni Marturano, Olga Dudchenko2

Sep 16

About misjoins correction step

Hey Giovanni, Please see page 17 of the Genome Assembly Cookbook (Figure 4) @ dnazoo.org/methods. (

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About misjoins correction step

Hey Giovanni, Please see page 17 of the Genome Assembly Cookbook (Figure 4) @ dnazoo.org/methods. (

Sep 16

Sep 16

Can't launch juicebox on mac, because I denied access to System Events.app

I get this same behavior on two macs, running Catalina and Mojave. I downloaded the 1.9.8.dmg from

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Can't launch juicebox on mac, because I denied access to System Events.app

I get this same behavior on two macs, running Catalina and Mojave. I downloaded the 1.9.8.dmg from

Sep 16

He Fang, … agho...@gmail.com8

Sep 15

Error while sorting

Hi Neva, Sorry for the confusion. I noticed after posting that the "echo "***! Error while

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Error while sorting

Hi Neva, Sorry for the confusion. I noticed after posting that the "echo "***! Error while

Sep 15

mushroom astar, Olga Dudchenko4

Sep 14

Can not use juicebox.2.13.05

Hello! First of all, I'm very glad to receive your reply! Now let me mainly show my problem！ 1.

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Can not use juicebox.2.13.05

Hello! First of all, I'm very glad to receive your reply! Now let me mainly show my problem！ 1.

Sep 14

Dustin Sokolowski, … C T14

Sep 14

Juicer as input for SALSA

Hello, Can someone please help me find the newer version of juicer_tools? I feel like I'm really

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Juicer as input for SALSA

Hello, Can someone please help me find the newer version of juicer_tools? I feel like I'm really

Sep 14

picas...@gmail.com, Olga Dudchenko2

Sep 14

Bad scaffolding. What others parameters can I tweak ?

Hello, Standard recommendation for this is to examine .0.hic and the associated tracks bed and wig

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Bad scaffolding. What others parameters can I tweak ?

Hello, Standard recommendation for this is to examine .0.hic and the associated tracks bed and wig

Sep 14

Xingbo Wu, Olga Dudchenko2

Sep 14

No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.

Hello Xingbo, Most likely there is a discrepancy between the names of the sequences in the fasta and

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No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.

Hello Xingbo, Most likely there is a discrepancy between the names of the sequences in the fasta and

Sep 14

tan...@gmail.com

Sep 14

about the resolution in HIC

Dear all, as I am aiming to identify promoter-enhancer loops in a HiC dataset by using resolutions of

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about the resolution in HIC

Dear all, as I am aiming to identify promoter-enhancer loops in a HiC dataset by using resolutions of

Sep 14

Marine Bergot, Neva Durand2

Sep 13

juicer issue too sparse to find many domains via Arrowhead

As the warning says: To disable sparsity check, use the --ignore-sparsity flag. On Mon, Sep 13, 2021

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juicer issue too sparse to find many domains via Arrowhead

As the warning says: To disable sparsity check, use the --ignore-sparsity flag. On Mon, Sep 13, 2021

Sep 13

Lyon Kingston, david Keens2

Sep 11

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Sep 11

Yunjiang Qiu, … Maoxuan Lin9

Sep 11

Eigenvector for higher resolution?

Hi Neva, I am running juicer_tools eigenvector for some higher resolutions and it is taking pretty

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Eigenvector for higher resolution?

Hi Neva, I am running juicer_tools eigenvector for some higher resolutions and it is taking pretty

Sep 11

Scott Ferguson, Olga Dudchenko4

Sep 10

Wig and Bed files

Hey Scott, I am sorry to say but your stats / 0.hic suggest a very bad library. All of your

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Wig and Bed files

Hey Scott, I am sorry to say but your stats / 0.hic suggest a very bad library. All of your

Sep 10

Ruchi Choudhary, Olga Dudchenko2

Sep 10

To find interactions associated with EBV genome in EBV infected cancer patients.

Hello, Yes it is possible. In fact you may already be doing it depending on the human reference you

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To find interactions associated with EBV genome in EBV infected cancer patients.

Hello, Yes it is possible. In fact you may already be doing it depending on the human reference you

Sep 10

Sep 8

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Sep 8

Sep 5

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Sep 5

kate, … Muhammad Saad Shamim4

Sep 5

Hello, --threads1 is working! Can I ask you one more question? I want to use CenterNormedAPA and APA

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Hello, --threads1 is working! Can I ask you one more question? I want to use CenterNormedAPA and APA

Sep 5

Pavla Navratilova, Olga Dudchenko6

Sep 2

Coversion of the annotation

After JBAT review you should run the 3D-DNA post-review script and generate the corresponding _HiC.

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Coversion of the annotation

After JBAT review you should run the 3D-DNA post-review script and generate the corresponding _HiC.

Sep 2

mushroom astar, Olga Dudchenko4

Sep 2

The result hic can not open

I would just start with trying to run on a larger machine perhaps. -Olga On Tuesday, August 31, 2021

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The result hic can not open

I would just start with trying to run on a larger machine perhaps. -Olga On Tuesday, August 31, 2021

Sep 2

m.t.l...@gmail.com, Olga Dudchenko2

Sep 2

I am not sure what you mean by assembly graph. Like a sequence overlap graph? That's usually used

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I am not sure what you mean by assembly graph. Like a sequence overlap graph? That's usually used

Sep 2

jay anh, … Olga Dudchenko4

Sep 1

Hello Jay, Not sure I understand your question. You are sayign that you used 3d-dna for de novo

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Hello Jay, Not sure I understand your question. You are sayign that you used 3d-dna for de novo

Sep 1

Azam Mohsin, … Muhammad Saad Shamim6

Aug 31

Are eigenvector values from juicer_tools flipped?

Each chromosome is independent. Unless you want to use the new script which takes care of this issue:

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Are eigenvector values from juicer_tools flipped?

Each chromosome is independent. Unless you want to use the new script which takes care of this issue:

Aug 31

Rosen Wen, Muhammad Saad Shamim3

Aug 30

Can hiccup not get the loop of 2K matrix?

Hey Rosen, Hope all is well. Sorry for the late reply. How was this file generated? By default, 5kb,

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Can hiccup not get the loop of 2K matrix?

Hey Rosen, Hope all is well. Sorry for the late reply. How was this file generated? By default, 5kb,

Aug 30

Aug 28

The result hic can not open

Hello! I used the 3d-dna/utils/wrap-fasta-sequence.awk <original.fasta> > wrapped.fasta.

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The result hic can not open

Hello! I used the 3d-dna/utils/wrap-fasta-sequence.awk <original.fasta> > wrapped.fasta.

Aug 28

Zhaoxi Liu, Olga Dudchenko4

Aug 27

Assembly file contains multiple entries of the same contig. Exiting!

Hi Dudchenko， Thank you for your advice! We realized the serious undercollapsed heterozygocity and

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Assembly file contains multiple entries of the same contig. Exiting!

Hi Dudchenko， Thank you for your advice! We realized the serious undercollapsed heterozygocity and

Aug 27

mushroom astar, Olga Dudchenko3

Aug 26

Question abou GNU Parallel to run 3D-DNA?

OK~ Thank you very much for your reply. I have now completed this step and it runs quicker than

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Question abou GNU Parallel to run 3D-DNA?

OK~ Thank you very much for your reply. I have now completed this step and it runs quicker than

Aug 26

mushroom astar, Olga Dudchenko3

Aug 26

A long time running 3D-DNA

OK~ Thank you very much for your reply. I have now completed this step and started a new attempt.

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A long time running 3D-DNA

OK~ Thank you very much for your reply. I have now completed this step and started a new attempt.

Aug 26

hc, Olga Dudchenko3

Aug 26

Phasing pipeline of 3D-DNA

Hi hc, Sorry for the delay in answering. What code have you been trying to run, the packaged one for

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Phasing pipeline of 3D-DNA

Hi hc, Sorry for the delay in answering. What code have you been trying to run, the packaged one for

Aug 26

F. Gözde Çilingir, Olga Dudchenko2

Aug 26

too many fragments despite improved contiguity of the assembly

Hi Gozde, Apologies for the delayed response. This is a great looking dataset and all looks good to

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too many fragments despite improved contiguity of the assembly

Hi Gozde, Apologies for the delayed response. This is a great looking dataset and all looks good to

Aug 26

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