Groups keyboard shortcuts have been updated

Dismiss

See shortcuts

3D Genomics

1–30 of 1976

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!

In order to filter spam, only members can post. Anyone can request to join the group, but please fill out a reason so that we can filter bots.

0 selected

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

unread,

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

Zihao Zhu, Moshe Olshansky8

3:02 AM

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

unread,

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

3:02 AM

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,

unread,

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 `

unread,

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

unread,

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

unread,

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

unread,

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

unread,

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

unread,

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

unread,

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

unread,

--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

unread,

[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.

unread,

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

unread,

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

unread,

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

unread,

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.

unread,

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

unread,

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

unread,

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 --

unread,

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

unread,

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 /

unread,

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

unread,

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

unread,

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

unread,

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

unread,

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

unread,

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

Feb 15

samyuktha Senthil

Feb 15

3d-DNA vote-order.awk error

Hello, I am using 3d-DNA to scaffold my draft assembly. Every time the run crashed with the following

unread,

3d-DNA vote-order.awk error

Hello, I am using 3d-DNA to scaffold my draft assembly. Every time the run crashed with the following

Feb 15

Debadeep Chaudhury, Moshe Olshansky4

Jan 30

Getting normalised matrices from hic files created using juicer_tools v2+

Thanks a lot for the info, I had no idea about the validate function of juicer_tools!! :) On Monday,

unread,

Getting normalised matrices from hic files created using juicer_tools v2+

Thanks a lot for the info, I had no idea about the validate function of juicer_tools!! :) On Monday,

Jan 30

ricar...@gmail.com, Moshe Olshansky3

Jan 29

Check .hic file for available normalization factors/values

thanks a lot. that did the trick! On Wednesday, January 29, 2025 at 4:40:07 PM UTC-5 moshe.o...@gmail

unread,

Check .hic file for available normalization factors/values

thanks a lot. that did the trick! On Wednesday, January 29, 2025 at 4:40:07 PM UTC-5 moshe.o...@gmail

Jan 29

Gaëlle LELANDAIS2

Jan 23

Problem with the visualization of the genome annotation on the HiC map

Good afternoon, I haven't received a reply to my message, so I'm taking the liberty of asking

unread,

Problem with the visualization of the genome annotation on the HiC map

Good afternoon, I haven't received a reply to my message, so I'm taking the liberty of asking

Jan 23

Search

Clear search

Close search

Google apps

Main menu