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, Juicer, 3D-DNA, JBAT, Straw, and more!

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Edoardo Marcora, Nasreen Bano2

7:20 PM

Conversion of HICCUPS loops bedpe files to BigInteract format

Hi Edoardo, Did you get the solution? I'm also looking for the same. Thank you, Nasreen On

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Conversion of HICCUPS loops bedpe files to BigInteract format

Hi Edoardo, Did you get the solution? I'm also looking for the same. Thank you, Nasreen On

7:20 PM

Rezwan Tariq, Levi Yant7

Apr 16

Juicer and 3DNA run for allotetraploid species

Hi team, Please share some suggestions on what sort of changes should I make in Juicer and 3D-DNA for

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Juicer and 3DNA run for allotetraploid species

Hi team, Please share some suggestions on what sort of changes should I make in Juicer and 3D-DNA for

Apr 16

Apr 16

Issue with Juicer Tools Pre: "Unable to find All-All or All-All"

Hi again, Since my previous message, I have actually managed to find why I was having such an error.

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Issue with Juicer Tools Pre: "Unable to find All-All or All-All"

Hi again, Since my previous message, I have actually managed to find why I was having such an error.

Apr 16

Apr 15

problem generating hic file using pre command

Hi, I am facing a problem generating hic file using pre command. I used the following command to

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problem generating hic file using pre command

Hi, I am facing a problem generating hic file using pre command. I used the following command to

Apr 15

Apr 13

How to convert processed contact matrix files to hic format

I have been viewing data available through encode as .hic data on the UCSC browser with great success

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How to convert processed contact matrix files to hic format

I have been viewing data available through encode as .hic data on the UCSC browser with great success

Apr 13

Lorenzo Bertola

Apr 10

Error generating HIC map with juicer tools pre - ArrayIndexOutOfBoundsException

Hello, I am trying to generate input files for manual curation of an assembly in Juicebox. I have 3

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Error generating HIC map with juicer tools pre - ArrayIndexOutOfBoundsException

Hello, I am trying to generate input files for manual curation of an assembly in Juicebox. I have 3

Apr 10

Christian Siadjeu

Apr 10

Merging Hi-C reads from different lanes

Hi everyone, I do have Hi-C reads from different lanes (forward and reverse). I would like to run

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Merging Hi-C reads from different lanes

Hi everyone, I do have Hi-C reads from different lanes (forward and reverse). I would like to run

Apr 10

Christopher Stehn

Apr 8

Difficulties calling loops with HiCCUPs

Hello! I have been trying to call loops using HiCCUPs in juicer_tools version 1.22.01. For my hic

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Difficulties calling loops with HiCCUPs

Hello! I have been trying to call loops using HiCCUPs in juicer_tools version 1.22.01. For my hic

Apr 8

Manohar Singh Bisht 2110105, Olga Dudchenko5

Apr 7

How to manually error correct the assembly in juicebox

Hi Olga, A gentle reminder! On Monday, January 22, 2024 at 3:40:20 PM UTC+5:30 Manohar Singh Bisht

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How to manually error correct the assembly in juicebox

Hi Olga, A gentle reminder! On Monday, January 22, 2024 at 3:40:20 PM UTC+5:30 Manohar Singh Bisht

Apr 7

Apr 4

How to deal with overlap part of scaffolds?

Dear Olga, I encountered this case, the scaffolds number is same as in our cytogenetic experment. But

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How to deal with overlap part of scaffolds?

Dear Olga, I encountered this case, the scaffolds number is same as in our cytogenetic experment. But

Apr 4

Apr 4

[After JBAT] What are the next steps

Hi Olga, I have edited the .hic maps and generated a .review.assembly from the initial rawchrom.

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[After JBAT] What are the next steps

Hi Olga, I have edited the .hic maps and generated a .review.assembly from the initial rawchrom.

Apr 4

Apr 4

Too many scaffolds

Hi there, I'm trying to use the 3d-dna pipeline to make my hifiasm assembly better (haplotype 1)

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Too many scaffolds

Hi there, I'm trying to use the 3d-dna pipeline to make my hifiasm assembly better (haplotype 1)

Apr 4

Cassandria Tay Fernandez

Apr 4

Restriction Enzyme file difference?

Hi Olga, My group has produced some high quality HiC and PacBio data and I've been trying to

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Restriction Enzyme file difference?

Hi Olga, My group has produced some high quality HiC and PacBio data and I've been trying to

Apr 4

Apr 3

Using FANC output .hic file in Juicebox?

Hello, Thank you for all the work you've been doing on this suite of tools. Real time browsing of

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Using FANC output .hic file in Juicebox?

Hello, Thank you for all the work you've been doing on this suite of tools. Real time browsing of

Apr 3

Sara Oppenheim, Olga Dudchenko3

Apr 3

visualizer format issue "Unexpected column count"

🤯 Hi Olga, my mnd is the "merged30.txt" output that juicer produced and stored in the

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visualizer format issue "Unexpected column count"

🤯 Hi Olga, my mnd is the "merged30.txt" output that juicer produced and stored in the

Apr 3

Apr 3

Interesting pattern in the contact map

Hi all, I want to first thank the developers and the community for this great set of tools for 3D

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Interesting pattern in the contact map

Hi all, I want to first thank the developers and the community for this great set of tools for 3D

Apr 3

Eric González, … Quentin ANDRES3

Apr 3

recommendations to obtain a haplotype-resolved assembly

Hi olga, how to duplicate pieces of the assembly in JBAT annotations? is it possible to do it within

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recommendations to obtain a haplotype-resolved assembly

Hi olga, how to duplicate pieces of the assembly in JBAT annotations? is it possible to do it within

Apr 3

guocen, Olga Dudchenko2

Apr 3

Jucier exit after the merged_nodups.txt file is created

Hi Cen, Yes, 3d-dna does not require any other input except for merged_nodups.txt file. Olga On

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Jucier exit after the merged_nodups.txt file is created

Hi Cen, Yes, 3d-dna does not require any other input except for merged_nodups.txt file. Olga On

Apr 3

Cara, … Rhianah sandean4

Apr 3

Arrowhead: 0 domains written to file

Hey all, Sorry to bring this up again, I am also stuck on the same problem, has anyone been able to

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Arrowhead: 0 domains written to file

Hey all, Sorry to bring this up again, I am also stuck on the same problem, has anyone been able to

Apr 3

Kristina Karandasheva

Apr 3

High percentage of Optical Duplicates

Hello everyone, I am currently using Juicer1.6 to process Hi-C experiment data and have encountered a

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High percentage of Optical Duplicates

Hello everyone, I am currently using Juicer1.6 to process Hi-C experiment data and have encountered a

Apr 3

Rhianah sandean, Karthick Babu Sivakumar4

Apr 2

Thank you! On Sunday 31 March 2024 at 06:51:56 UTC+1 karthick...@pau.edu wrote: Check assembly

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Thank you! On Sunday 31 March 2024 at 06:51:56 UTC+1 karthick...@pau.edu wrote: Check assembly

Apr 2

Quentin ANDRES, Olga Dudchenko5

Apr 2

No real time update of the Hi-C matrix ?

Hi Olga, Do you mean that the best way to edit hic assemblies in Juicer is to use juicer_tools v2.

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No real time update of the Hi-C matrix ?

Hi Olga, Do you mean that the best way to edit hic assemblies in Juicer is to use juicer_tools v2.

Apr 2

Megan H, Mohan Govindasamy3

Mar 29

Code trying to pull from a path that does not exist.

Can you try installing gawk and try again? On Saturday, February 10, 2024 at 1:56:13 AM UTC Megan H

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Code trying to pull from a path that does not exist.

Can you try installing gawk and try again? On Saturday, February 10, 2024 at 1:56:13 AM UTC Megan H

Mar 29

Mohan Govindasamy2

Mar 29

Error in creating .hic file

I was able to figure out what went wrong here—something to do with using multithreading when creating

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Error in creating .hic file

I was able to figure out what went wrong here—something to do with using multithreading when creating

Mar 29

Mar 28

Jucier LSF exit after merged_nodups.txt file is created

Hi everyone, I was running juicer-1.6 LSF scripts and exited after the merged_nodups.txt file was

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Jucier LSF exit after merged_nodups.txt file is created

Hi everyone, I was running juicer-1.6 LSF scripts and exited after the merged_nodups.txt file was

Mar 28

Rezwan Tariq, Olga Dudchenko6

Mar 22

How can I improve the Hi-C plot

Hi Olga, Is the polishing meant regarding assembly polishing or curation of chromosomes with juicebox

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How can I improve the Hi-C plot

Hi Olga, Is the polishing meant regarding assembly polishing or curation of chromosomes with juicebox

Mar 22

Alexiy Boyko, Olga Dudchenko2

Mar 19

About Hi-C scaffolding with libraries from different individuals

Hi, I imagine if you have a species with high recombination/rearrangement prevalance it would

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About Hi-C scaffolding with libraries from different individuals

Hi, I imagine if you have a species with high recombination/rearrangement prevalance it would

Mar 19

Jiangjiang Zhang, Olga Dudchenko2

Mar 19

I assembly the genome with juicer and 3d-dna, when run the command "run-asm-pipeline.sh -r 0 raw_scaffold_2.fasta ./aligned/merged_nodups.txt"

Do you have anything in you .0.hic file? I would check that the fasta has no weird newline characters

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I assembly the genome with juicer and 3d-dna, when run the command "run-asm-pipeline.sh -r 0 raw_scaffold_2.fasta ./aligned/merged_nodups.txt"

Do you have anything in you .0.hic file? I would check that the fasta has no weird newline characters

Mar 19

Megan H, Olga Dudchenko3

Mar 19

3D-DNA - how many GB are needed to run?

This can happen if you have a very large genome and a very fragmented draft. You can remove all h.

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3D-DNA - how many GB are needed to run?

This can happen if you have a very large genome and a very fragmented draft. You can remove all h.

Mar 19

Gian Marco Franceschini, Olga Dudchenko2

Mar 19

How to remove small chromosomes from .hic files

Create a chrom.sizes file that will only contain the chromosomes you would like to retain and pass

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How to remove small chromosomes from .hic files

Create a chrom.sizes file that will only contain the chromosomes you would like to retain and pass

Mar 19

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