3D Genomics

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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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Helen, … Mark Mackiewicz3

Jul 26

Problem visualizing output (.hic files) in UCSC

I have run into the same problem as Helen, is there a workaround solution for this? Thanks, Mark On

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Problem visualizing output (.hic files) in UCSC

I have run into the same problem as Helen, is there a workaround solution for this? Thanks, Mark On

Jul 26

F. Gözde Çilingir

Jul 26

too many fragments despite improved contiguity of the assembly

Hello, Thank you very much for these super useful tools. I have been working on the chromosome-level

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too many fragments despite improved contiguity of the assembly

Hello, Thank you very much for these super useful tools. I have been working on the chromosome-level

Jul 26

mushroom astar, Neva Durand3

Jul 26

Long running Juicer

Hello! I am using the CPU version of juicer1.6. When I enter juicer.sh - h, the - C option does not

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Long running Juicer

Hello! I am using the CPU version of juicer1.6. When I enter juicer.sh - h, the - C option does not

Jul 26

Jul 25

Arrowhead: 0 domains written to file

Hi Team, To follow up on my last question, I tried every resolution that arrowhead accepted, still

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Arrowhead: 0 domains written to file

Hi Team, To follow up on my last question, I tried every resolution that arrowhead accepted, still

Jul 25

Jul 23

Phasing pipeline of 3D-DNA

Hi when I ran run-hic-phaser.sh, it reported: :) Parsing vcf file... mv: cannot stat 'in.assembly

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Phasing pipeline of 3D-DNA

Hi when I ran run-hic-phaser.sh, it reported: :) Parsing vcf file... mv: cannot stat 'in.assembly

Jul 23

Matthew Tegtmeyer

Jul 20

Retaining CNV signatures

Hello, I'm trying to explore the impact of a large CNV on genome structure. When i visualize the

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Retaining CNV signatures

Hello, I'm trying to explore the impact of a large CNV on genome structure. When i visualize the

Jul 20

Jun Kim, … Matt Romero5

Jul 19

normalization for visualizing two samples

Hi Muhammad and Jun, Thanks so much for the info! I did use the VS mode in juicebox and that seems to

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normalization for visualizing two samples

Hi Muhammad and Jun, Thanks so much for the info! I did use the VS mode in juicebox and that seems to

Jul 19

Tay, Neva Durand2

Jul 19

Visualizing a single trans chromosomal loop

Hello, Have you tried just looking at the file in Juicebox? aidenlab.org/juicebox On Sat, Jul 17,

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Visualizing a single trans chromosomal loop

Hello, Have you tried just looking at the file in Juicebox? aidenlab.org/juicebox On Sat, Jul 17,

Jul 19

Jul 19

Can hiccup not get the loop of 2K matrix?

I try to use pre to generate 2K matrix (HIC file), and use hiccups to calculate the loops of the

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Can hiccup not get the loop of 2K matrix?

I try to use pre to generate 2K matrix (HIC file), and use hiccups to calculate the loops of the

Jul 19

Jul 16

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Jul 16

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Jul 16

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Jul 16

Sadman Sakib, Muhammad Saad Shamim3

Jul 15

Getting ArrayIndexOutOfBoundsException When Running CPU HiCCUPS

Hello, Thanks for the quick reply! I have tried with --threads 1. Unfortunately, I'm getting the

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Getting ArrayIndexOutOfBoundsException When Running CPU HiCCUPS

Hello, Thanks for the quick reply! I have tried with --threads 1. Unfortunately, I'm getting the

Jul 15

philil...@gmail.com, Olga Dudchenko2

Jul 9

Inputs for the phasing module

Hi Philip, You only need to contig reads if you don't have a reference assembly: if you are

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Inputs for the phasing module

Hi Philip, You only need to contig reads if you don't have a reference assembly: if you are

Jul 9

Yonatan Amzaleg, Neva Durand4

Jul 8

Juicer pipeline to try other loop calling programs

For a dedupped bam file, it's best to use Juicer2, which can be found on the ENCODE branch of the

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Juicer pipeline to try other loop calling programs

For a dedupped bam file, it's best to use Juicer2, which can be found on the ENCODE branch of the

Jul 8

Ian D, Neva Durand5

Jul 8

How to convert a HG19 Hi-C hic file to HG38?

Thank you. I found the SRA files after being prompted my your last reply. That route sounds much

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How to convert a HG19 Hi-C hic file to HG38?

Thank you. I found the SRA files after being prompted my your last reply. That route sounds much

Jul 8

Neva Durand, … etiennedanis10

Jul 7

Re: can't creat temporary file HIC_tmp

I 3IAM n Sent from my T-Mobile 4G LTE Device 3w -------- Orig jminal message -------- From: '

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Re: can't creat temporary file HIC_tmp

I 3IAM n Sent from my T-Mobile 4G LTE Device 3w -------- Orig jminal message -------- From: '

Jul 7

YT Chen, Olga Dudchenko4

Jul 7

The contact map is only half size of my assembly

Hi Olga, Thank you very much for your explanation. The picture is 0.hic. The Hi-C data were passed to

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The contact map is only half size of my assembly

Hi Olga, Thank you very much for your explanation. The picture is 0.hic. The Hi-C data were passed to

Jul 7

Arielle Johnson, Olga Dudchenko3

Jul 6

Tweaking parameters for 330 Mb plant Hi-C run

Hi Olga, Thanks so much for the quick response! I had read the Genome Assembly Cookbook and the

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Tweaking parameters for 330 Mb plant Hi-C run

Hi Olga, Thanks so much for the quick response! I had read the Genome Assembly Cookbook and the

Jul 6

tan...@gmail.com, … Neil Young18

Jul 4

using HIC pipeline on HIC data from ARIMA GENOMICS

I love this forum! I was looking at using juicer with the new Arima 4 enzyme high coverage kit.

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using HIC pipeline on HIC data from ARIMA GENOMICS

I love this forum! I was looking at using juicer with the new Arima 4 enzyme high coverage kit.

Jul 4

linyong shen, Neva Durand5

Jul 4

Question about'/aligned/inter.txt'

Thank you very much, I have found the perfect solution, using "bash juicer" instead of

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Question about'/aligned/inter.txt'

Thank you very much, I have found the perfect solution, using "bash juicer" instead of

Jul 4

Arushi Khanna, … Berkley Gryder6

Jul 3

Assembly unable to align in Juicebox

Olga, Arushi: I am going to try to rebuild the .hic files from the fasta using juicer tools, rather

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Assembly unable to align in Juicebox

Olga, Arushi: I am going to try to rebuild the .hic files from the fasta using juicer tools, rather

Jul 3

Jul 1

eigenvector values flipped

Hi, I notice that for some of our HiC samples visualized on juicebox, the eigenvector values are

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eigenvector values flipped

Hi, I notice that for some of our HiC samples visualized on juicebox, the eigenvector values are

Jul 1

Cara, Neva Durand2

Jun 30

TAD regions visualization in Juicebox

Yes, we use the bedpe format. This is detailed here: https://github.com/aidenlab/Juicebox/wiki/

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TAD regions visualization in Juicebox

Yes, we use the bedpe format. This is detailed here: https://github.com/aidenlab/Juicebox/wiki/

Jun 30

Avrami Aharonoff, John Urban3

Jun 27

SBATCH error when running juicer

I did end up figuring it out. Learned what a partition is and what the names of the partitions are on

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SBATCH error when running juicer

I did end up figuring it out. Learned what a partition is and what the names of the partitions are on

Jun 27

andrea.p...@msn.com, Neva Durand2

Jun 25

Empty inter.txt file

Either something went wrong with chimera handling or it's having trouble finding the *norm*res.

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Empty inter.txt file

Either something went wrong with chimera handling or it's having trouble finding the *norm*res.

Jun 25

yliu, Neva Durand2

Jun 25

download normalization vector

Sorry for the late reply. Just use Juicer Tools dump norm. On Wed, May 26, 2021 at 1:43 AM 'yliu

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download normalization vector

Sorry for the late reply. Just use Juicer Tools dump norm. On Wed, May 26, 2021 at 1:43 AM 'yliu

Jun 25

Erin Zampaglione, Neva Durand3

Jun 24

Can't upload a bed file to juicebox

Hi Neva, Thank you so much for responding! Oh my goodness, I can't believe it - I didn't

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Can't upload a bed file to juicebox

Hi Neva, Thank you so much for responding! Oh my goodness, I can't believe it - I didn't

Jun 24

hamidc...@gmail.com, … Neva Durand3

Jun 22

Conversion of HiC files to BigInteract

You can load hic files directly into the UCSC browser On Tue, Jun 22, 2021 at 11:16 AM Edoardo

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Conversion of HiC files to BigInteract

You can load hic files directly into the UCSC browser On Tue, Jun 22, 2021 at 11:16 AM Edoardo

Jun 22

Nate Backenstose, Olga Dudchenko4

Jun 22

Optimizing scaffolding of a genome with tetrasomic inheritance

Hi Nate, Great job exploring the issues of parameter adjustment on the forum! Looking at your data I

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Optimizing scaffolding of a genome with tetrasomic inheritance

Hi Nate, Great job exploring the issues of parameter adjustment on the forum! Looking at your data I

Jun 22

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