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3D Genomics

1–30 of 1980

Welcome to the Aiden Lab's forum for all questions, comments, and concerns relating to 3D Genomics, including the Hi-C protocol, Juicebox, Juicer, 3D-DNA, JBAT, Straw, and more!

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Olga Dudchenko, … Md Waqar Alam3

5/8/20

Welcome to the DNA Zoo!

On Thursday, 6 December 2018 15:34:15 UTC+5:30, Olga Dudchenko wrote: Dear friends, We are thrilled

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Welcome to the DNA Zoo!

On Thursday, 6 December 2018 15:34:15 UTC+5:30, Olga Dudchenko wrote: Dear friends, We are thrilled

5/8/20

Jun 13

Juicer Question

I cannot get Juicer to align my files post splitting. It does the first set of fastq files and then

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Juicer Question

I cannot get Juicer to align my files post splitting. It does the first set of fastq files and then

Jun 13

Jun 13

Juicer not correctly assigning/aligning SAM file for each FASTQ split file

I am running Juicer Slurm juicer.sh on a large Hi-C fastq file set (R1 is 66GB and R2 is 73 GB).

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Juicer not correctly assigning/aligning SAM file for each FASTQ split file

I am running Juicer Slurm juicer.sh on a large Hi-C fastq file set (R1 is 66GB and R2 is 73 GB).

Jun 13

Dr.Mohamed.Salama

Jun 4

Add Haploview Linkage Disequilibrium to UCSC B38

Hi, Sorry, but I am very new to this. I am trying to add Haploview Linkage Disequilibrium data as a

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Add Haploview Linkage Disequilibrium to UCSC B38

Hi, Sorry, but I am very new to this. I am trying to add Haploview Linkage Disequilibrium data as a

Jun 4

samyuktha Senthil

May 19

Final files for interpretation

Hi, Thanks for this wonderful tool, it is my first time using 3d-DNA. I have a small doubt, which is

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Final files for interpretation

Hi, Thanks for this wonderful tool, it is my first time using 3d-DNA. I have a small doubt, which is

May 19

Zihao Zhu, Moshe Olshansky8

May 17

speeding up processing for a large input file

Hi Zihaom Sorry for the delay. Your files look right. You can run java -jar your_juicer_tools.jar

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speeding up processing for a large input file

Hi Zihaom Sorry for the delay. Your files look right. You can run java -jar your_juicer_tools.jar

May 17

May 11

Reverse conversion from .hic to merged_nodups.txt

Dear developers, I would like to perform an aggregate chromosome analysis as in Hoecamp et al., 2021,

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Reverse conversion from .hic to merged_nodups.txt

Dear developers, I would like to perform an aggregate chromosome analysis as in Hoecamp et al., 2021,

May 11

Aman Shamil, … Alice Laigle3

May 11

Hi Aman, It might be too late, but in case: to convert .hic files to .cool, I used the `

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Hi Aman, It might be too late, but in case: to convert .hic files to .cool, I used the `

May 11

Nguyen Xuan-Thang2

May 9

set up for the Juicer genome draft assembly on HPC

Here is my change for the code of juicer.sh, but the errors is jobdependency shopt -s extglob

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set up for the Juicer genome draft assembly on HPC

Here is my change for the code of juicer.sh, but the errors is jobdependency shopt -s extglob

May 9

May 8

Is there any way to convert .hic to bedpe with juicer tools ? I want to extract intra and inter

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Is there any way to convert .hic to bedpe with juicer tools ? I want to extract intra and inter

May 8

May 8

Empty post processed pixels

Hi, I am working with Juicer hiccups for finding loops, using the following command java -Xmx32g -jar

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Empty post processed pixels

Hi, I am working with Juicer hiccups for finding loops, using the following command java -Xmx32g -jar

May 8

May 7

Introduction to Genome Annotation - online course

Dear all, there are only a few seats left for our upcoming online course: Introduction to Genome

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Introduction to Genome Annotation - online course

Dear all, there are only a few seats left for our upcoming online course: Introduction to Genome

May 7

Shirlekar, Kalyanee, Moshe Olshansky2

Apr 30

Hi Kalyanee, This is an interesting and important question to which I don't know the answer. I

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Hi Kalyanee, This is an interesting and important question to which I don't know the answer. I

Apr 30

Apr 22

Good evening. Overall, I think my output looks decent in Juicer. I do have 2 situations - 1 being a

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Good evening. Overall, I think my output looks decent in Juicer. I do have 2 situations - 1 being a

Apr 22

Apr 17

--cpu option unavailable on docker

I am attempting to run this .hic file -> https://www.ncbi.nlm.nih.gov/sra/SRX5247015[accn] through

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--cpu option unavailable on docker

I am attempting to run this .hic file -> https://www.ncbi.nlm.nih.gov/sra/SRX5247015[accn] through

Apr 17

Apr 17

[3D-DNA] gawk:fatal error, scrape-mnd.awk:13: atal error,

Hello! I've been trying to run the run-asm-pipeline.sh with 4.5Gb genome.fa and 379Gb

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[3D-DNA] gawk:fatal error, scrape-mnd.awk:13: atal error,

Hello! I've been trying to run the run-asm-pipeline.sh with 4.5Gb genome.fa and 379Gb

Apr 17

Apr 11

Problem of splitting the Scaffold

Hello! I want to split this scaffold below in the graph, for it shows low frequency of contact.

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Problem of splitting the Scaffold

Hello! I want to split this scaffold below in the graph, for it shows low frequency of contact.

Apr 11

Мария Нечеухина

Apr 7

the problem with the encoding of the hic file

I use juicer version 2.0 and juicer_tools.version 2.09.00. I get a translation of the resulting

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the problem with the encoding of the hic file

I use juicer version 2.0 and juicer_tools.version 2.09.00. I get a translation of the resulting

Apr 7

SEBASTIAN DONOSO, Beisi Xu4

Apr 7

X-Shaped Pattern in Juicebox Visualization

Yes, the genome shown in the figure contains about 34% transposable elements, and from what I

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X-Shaped Pattern in Juicebox Visualization

Yes, the genome shown in the figure contains about 34% transposable elements, and from what I

Apr 7

Apr 5

Online course: Comparative Genomics -- 7-11 April

Dear all, Only a few seats are remaining for the upcoming Physalia online course: Comparative

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Online course: Comparative Genomics -- 7-11 April

Dear all, Only a few seats are remaining for the upcoming Physalia online course: Comparative

Apr 5

Samuel Kean, Beisi Xu2

Apr 3

Empty .hic file using Juicer pre

maybe merged_nodups.txt corrupted. does each line have the same number of fields? cat merged_nodups.

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Empty .hic file using Juicer pre

maybe merged_nodups.txt corrupted. does each line have the same number of fields? cat merged_nodups.

Apr 3

Lu Yin, … Alicia45

Mar 20

Juicer results issues

Dear Olga, My name is Alicia, and I am trying to use your software to scaffold a draft genome. I am

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Juicer results issues

Dear Olga, My name is Alicia, and I am trying to use your software to scaffold a draft genome. I am

Mar 20

Mar 11

JuiceBox Assembly Tools

Hello, I am new to genome assembly. I just started using JBAT. I have a question. If a region is

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JuiceBox Assembly Tools

Hello, I am new to genome assembly. I just started using JBAT. I have a question. If a region is

Mar 11

Mar 10

Using juicer to process HIRES data

Hello every guys,Over the past few days I have tried using the following code: cutadapt --discard --

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Using juicer to process HIRES data

Hello every guys,Over the past few days I have tried using the following code: cutadapt --discard --

Mar 10

Mar 2

Correct format for Hi-C matrix before converting to BEDPE

I am working with interchromosomal Hi-C interaction data and need to extract a matrix from a .hic

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Correct format for Hi-C matrix before converting to BEDPE

I am working with interchromosomal Hi-C interaction data and need to extract a matrix from a .hic

Mar 2

Isabella Pirozzolo

Feb 25

Diploid.sh CPU error

Hi all - I am running diploid.sh using path/to/juicer/juicer-1.6/CPU/common/diploid.sh -g mm10 -s /

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Diploid.sh CPU error

Hi all - I am running diploid.sh using path/to/juicer/juicer-1.6/CPU/common/diploid.sh -g mm10 -s /

Feb 25

Feb 25

lower N50 after running 3D-DNA

Hi all, I used hifiasm to assemble primary genome (estimated size 2.5G) with HiFi data and ONT utra

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lower N50 after running 3D-DNA

Hi all, I used hifiasm to assemble primary genome (estimated size 2.5G) with HiFi data and ONT utra

Feb 25

Feb 22

Online course - Epigenomics Data Analysis - April 14-18

Dear all, We are pleased to announce our upcoming online course: Epigenomics Data Analysis, taking

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Online course - Epigenomics Data Analysis - April 14-18

Dear all, We are pleased to announce our upcoming online course: Epigenomics Data Analysis, taking

Feb 22

Feb 15

How to reflect the sequence IDs in final *HiC.fasta file to .assembly and .hic files?

Hi, I would like to visualize the results of 3D-DNA using software such as HiCPlotter. In our routine

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How to reflect the sequence IDs in final *HiC.fasta file to .assembly and .hic files?

Hi, I would like to visualize the results of 3D-DNA using software such as HiCPlotter. In our routine

Feb 15

Мария Нечеухина

Feb 15

resolution of Hi-C matrix

I created a hic file using Juicer. How to set the map resolution. In Juicebox, I see a maximum

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resolution of Hi-C matrix

I created a hic file using Juicer. How to set the map resolution. In Juicebox, I see a maximum

Feb 15

samyuktha Senthil

Feb 15

Hi, I am using 3d-DNA to scaffold my draft assembly. The pipeline crashes at the merge step with the

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Hi, I am using 3d-DNA to scaffold my draft assembly. The pipeline crashes at the merge step with the

Feb 15

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