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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Holden Leung, … Moshe Olshansky6

Nov 20

Issue with dumping KR matrix

Hello, You should use juicer_tools pre without normalization and then add norm manually with addNorm

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Issue with dumping KR matrix

Hello, You should use juicer_tools pre without normalization and then add norm manually with addNorm

Nov 20

Nov 20

concerning genic content of superscaffold based on BUSCO

Hi Olga and Aiden Lab team, It's my first time making a genome assembly and the educational

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concerning genic content of superscaffold based on BUSCO

Hi Olga and Aiden Lab team, It's my first time making a genome assembly and the educational

Nov 20

Aditya Shrivastava, Olga Dudchenko4

Nov 19

Compatibility of 3D-CARTA with Juicer 2.0

Hi Aditya, It should be possible to use any sam files including those generated by Juicer2 from Hi-C.

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Compatibility of 3D-CARTA with Juicer 2.0

Hi Aditya, It should be possible to use any sam files including those generated by Juicer2 from Hi-C.

Nov 19

Dearbhaile Casey, Olga Dudchenko2

Nov 19

Covergae spanning the entire assembly

Hi Deabhaile, It is hard to say from just looking at it. If this is a primary sample this may be some

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Covergae spanning the entire assembly

Hi Deabhaile, It is hard to say from just looking at it. If this is a primary sample this may be some

Nov 19

Dearbhaile Casey

Nov 19

Coverage spanning entire assembly

Hi, Would you be able to help me understand what is going on this map. What is the coverage spanning

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Coverage spanning entire assembly

Hi, Would you be able to help me understand what is going on this map. What is the coverage spanning

Nov 19

Ahmed Abbas, Gilbert Han5

Nov 12

Question about QC of HiCut sample

This is puzzling. In the HiCUT paper, they filtered short-range contacts to identify loops. One

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Question about QC of HiCut sample

This is puzzling. In the HiCUT paper, they filtered short-range contacts to identify loops. One

Nov 12

Nov 4

Trouble running arrowhead on ENCODE portal .hic files

Nevermind. "VC-SQRT" should have been "VC_SQRT". Sorry for the mistake. On Monday

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Trouble running arrowhead on ENCODE portal .hic files

Nevermind. "VC-SQRT" should have been "VC_SQRT". Sorry for the mistake. On Monday

Nov 4

KB Paton, Olga Dudchenko5

Nov 4

Unable to export modified assembly to fasta

Hi Olga, Okay, thank you, that's clear. I will need to do some more work myself to see where I

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Unable to export modified assembly to fasta

Hi Olga, Okay, thank you, that's clear. I will need to do some more work myself to see where I

Nov 4

Cynthia Chen, Olga Dudchenko2

Oct 31

Cannot generate output files with juicebox_assembly_converter.py

I do not know the script juicebox_assembly_converter.py. This is not our script, sorry. -Olga

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Cannot generate output files with juicebox_assembly_converter.py

I do not know the script juicebox_assembly_converter.py. This is not our script, sorry. -Olga

Oct 31

Vikram Iyer, Olga Dudchenko2

Oct 31

Error in Juicer for genome assembly

You do not need the hic file for assembly. You only need the merged_nodups.txt file. See the genome

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Error in Juicer for genome assembly

You do not need the hic file for assembly. You only need the merged_nodups.txt file. See the genome

Oct 31

Oct 11

Error: the chromosome combination 1_2 appears in multiple blocks

ohhhh i thought i've found whats wrong. i must sort fragments by the position! now everything

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Error: the chromosome combination 1_2 appears in multiple blocks

ohhhh i thought i've found whats wrong. i must sort fragments by the position! now everything

Oct 11

Ryan Martinez, Olga Dudchenko5

Oct 9

0.hic looks better than final.hic?

Just finished running BUSCO on the two assemblies as well. I do feel like a 2.3% reduction in the

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0.hic looks better than final.hic?

Just finished running BUSCO on the two assemblies as well. I do feel like a 2.3% reduction in the

Oct 9

Aditya Shrivastava

Oct 7

Interpretation of Non-Conserved Changes in A/B Compartments

I am currently analyzing Hi-C data from several species, which I have mapped onto a closely related

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Interpretation of Non-Conserved Changes in A/B Compartments

I am currently analyzing Hi-C data from several species, which I have mapped onto a closely related

Oct 7

Sep 26

Question about Micro-c

Hi all！here is my question : Why Micro-C typically uses paired-end sequencing of 100bp or 50bp rather

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Question about Micro-c

Hi all！here is my question : Why Micro-C typically uses paired-end sequencing of 100bp or 50bp rather

Sep 26

Sep 23

Support of non-fixed bin sizes

I am trying to get the interactions of cis-regulatory regions, therefore I want to know if juicer

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Support of non-fixed bin sizes

I am trying to get the interactions of cis-regulatory regions, therefore I want to know if juicer

Sep 23

evolution, Olga Dudchenko3

Sep 17

NNNCTTAAGNN_pattern

Hi Ogla I found those come from optical mapping ..these are optical mapping restriction sites. On

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NNNCTTAAGNN_pattern

Hi Ogla I found those come from optical mapping ..these are optical mapping restriction sites. On

Sep 17

Yue Yu, Olga Dudchenko2

Sep 16

Odd vertical and horizontal line in Hi-C contact map, why?

This is most likely a two-color chemistry sequencing artifact, not a real 3D contact artifact. Best,

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Odd vertical and horizontal line in Hi-C contact map, why?

This is most likely a two-color chemistry sequencing artifact, not a real 3D contact artifact. Best,

Sep 16

Aditya Shrivastava, Olga Dudchenko2

Sep 16

Implementation of Dual Restriction Enzyme in 3D-CARTA

Hi, We have not directly tested this but in theory you should be able pass multiple restriction

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Implementation of Dual Restriction Enzyme in 3D-CARTA

Hi, We have not directly tested this but in theory you should be able pass multiple restriction

Sep 16

shunda li, Olga Dudchenko2

Sep 16

manual curation

That depends on what you investigate is a reason for the white area. If this is a mapping issue but a

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manual curation

That depends on what you investigate is a reason for the white area. If this is a mapping issue but a

Sep 16

Guy Horev, Olga Dudchenko4

Sep 16

Assitance with Hi-C contact map interpretation

Hi Guy, Unfortunately we do not have bandwidth to comment on specific maps and guide edits via the

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Assitance with Hi-C contact map interpretation

Hi Guy, Unfortunately we do not have bandwidth to comment on specific maps and guide edits via the

Sep 16

Giacomo M, Olga Dudchenko2

Sep 16

Sexual chromosome in Eulemur mongoz assembly

Hi Giacomo, Based on the readme HiC_scaffold_30 should be X. 31 should be Y. -Olga On Tuesday, August

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Sexual chromosome in Eulemur mongoz assembly

Hi Giacomo, Based on the readme HiC_scaffold_30 should be X. 31 should be Y. -Olga On Tuesday, August

Sep 16

Nick Jeffery, Olga Dudchenko2

Sep 16

juicer 2.0 can't use my fastq.gz files

Do your fastq files match the _R1* _R2* format? It looks like you might have file naming issues. -

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juicer 2.0 can't use my fastq.gz files

Do your fastq files match the _R1* _R2* format? It looks like you might have file naming issues. -

Sep 16

Sep 10

Genome ID Issue when Using Public HiC Datasets

Dear develop team: Thanks so much for the development and maintenance for juicer community. I've

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Genome ID Issue when Using Public HiC Datasets

Dear develop team: Thanks so much for the development and maintenance for juicer community. I've

Sep 10

Sep 5

Homer Hi-C analysis

What is the input file required to find the correlation difference between 2 experiments using

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Homer Hi-C analysis

What is the input file required to find the correlation difference between 2 experiments using

Sep 5

Aug 25

About multiple restriction sites

Hi 3D Genomics group, The restriction sites used in my hic library construction were AG^CT and TG^CA.

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About multiple restriction sites

Hi 3D Genomics group, The restriction sites used in my hic library construction were AG^CT and TG^CA.

Aug 25

Aug 23

JAVA- .hic file

Hi everyone, I am trying to generate the .hic file, but I encountered a problem: "Disk quota

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JAVA- .hic file

Hi everyone, I am trying to generate the .hic file, but I encountered a problem: "Disk quota

Aug 23

Jeffrey Chiu, Olga Dudchenko3

Aug 22

How Does Computation Time Scale with Input File Size in Genome Assembly?

Got it. Thank you. On Monday, August 19, 2024 at 10:13:34 PM UTC-7 Olga Dudchenko wrote: The

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How Does Computation Time Scale with Input File Size in Genome Assembly?

Got it. Thank you. On Monday, August 19, 2024 at 10:13:34 PM UTC-7 Olga Dudchenko wrote: The

Aug 22

Saumya, … Aditya Shrivastava8

Aug 22

eigenvector output file is empty

Dear Olga and Moshe, Thank you for your guidance. Regards Aditya Shrivastava On Tuesday 20 August

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eigenvector output file is empty

Dear Olga and Moshe, Thank you for your guidance. Regards Aditya Shrivastava On Tuesday 20 August

Aug 22

xiaolei zhou, Olga Dudchenko2

Aug 20

How can I merge and visualize data from two biological replicates in juicebox

Look into the mega.sh script. -Olga On Sunday, August 11, 2024 at 9:37:22 PM UTC-5 xiaolei...@gmail.

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How can I merge and visualize data from two biological replicates in juicebox

Look into the mega.sh script. -Olga On Sunday, August 11, 2024 at 9:37:22 PM UTC-5 xiaolei...@gmail.

Aug 20

Aug 18

Assistance with Hi-C contact map interpretation

Hi, I hope I don't start a redundant conversation, I don't see my 1st message. I am working

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Assistance with Hi-C contact map interpretation

Hi, I hope I don't start a redundant conversation, I don't see my 1st message. I am working

Aug 18

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