HiC-Pro

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Welcome to the HiC-Pro forum. Feel free to ask any question, repots bugs, idea or any other comments !
HiC-Pro is an optimized and flexible pipeline for Hi-C data processing. HiC-Pro is freely available at https://github.com/nservant/HiC-Pro
Manual is available at http://nservant.github.io/HiC-Pro/

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Feb 19

Hi, My apologies if this question sounds naive, as I have recently started to learn the pipeline. I

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Hi, My apologies if this question sounds naive, as I have recently started to learn the pipeline. I

Feb 19

Miao Wang, nservant2

Jan 26

Merge allValidPairs and convert to .hic

yes absolutely On Sunday 14 January 2024 at 21:02:26 UTC+1 mw3...@columbia.edu wrote: Hi Can I use

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Merge allValidPairs and convert to .hic

yes absolutely On Sunday 14 January 2024 at 21:02:26 UTC+1 mw3...@columbia.edu wrote: Hi Can I use

Jan 26

12/1/23

how to continue after mapping r1 and r1

Hello, Due to a server reboot problem, HiC-Pro running stopped after completing Bowtie2 alignment

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how to continue after mapping r1 and r1

Hello, Due to a server reboot problem, HiC-Pro running stopped after completing Bowtie2 alignment

12/1/23

11/2/23

Hello. I an running the HiC-Pro on a cluster. After I modify the config.txt I run the pipeline and

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Hello. I an running the HiC-Pro on a cluster. After I modify the config.txt I run the pipeline and

11/2/23

7/29/23

High proportion of duplicates(%) in valid pairs

Hi nservant, I am using HiC-Pro to process my HiC raw data. After alignment and filtering, I got some

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High proportion of duplicates(%) in valid pairs

Hi nservant, I am using HiC-Pro to process my HiC raw data. After alignment and filtering, I got some

7/29/23

5/8/23

bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

Hi , I am trying to process HepG2 cell line ENCODE data using all 10 replicates (5 each from two

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bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

Hi , I am trying to process HepG2 cell line ENCODE data using all 10 replicates (5 each from two

5/8/23

2/13/23

No results or errors when running HiC-Pro

Hello, I am trying to use HiC-Pro to analyze HiChIP data. When I try to run HiC-Pro, it runs for a

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No results or errors when running HiC-Pro

Hello, I am trying to use HiC-Pro to analyze HiChIP data. When I try to run HiC-Pro, it runs for a

2/13/23

Helene Bordelet

1/17/23

trans G1-G2 contacts in allele specific mode

Hi, I am a new user of HiC-pro and I am particularly interested in the allele specific module. I

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trans G1-G2 contacts in allele specific mode

Hi, I am a new user of HiC-pro and I am particularly interested in the allele specific module. I

1/17/23

Clifford Rostomily, … maharshich...@gmail.com6

1/13/23

Quality pairs with singleton not mapping

Hey, Sorry I did not try this, and have not been working on this project. I believe someone in the

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Quality pairs with singleton not mapping

Hey, Sorry I did not try this, and have not been working on this project. I believe someone in the

1/13/23

11/21/22

Merge of technical replicates

Hi, Is there a way in HiC-Pro to merge technical replicates? For instance I am analysing already

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Merge of technical replicates

Hi, Is there a way in HiC-Pro to merge technical replicates? For instance I am analysing already

11/21/22

11/21/22

Choosing bin settings

Hi, I want to run HiC-Pro to detect interactions at single gene level. I am writing in the case

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Choosing bin settings

Hi, I want to run HiC-Pro to detect interactions at single gene level. I am writing in the case

11/21/22

11/21/22

conda: command not found

Hi, I am running into this issue /usr/share/lmod/lmod/init/bash: line 163: conda: command not found /

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conda: command not found

Hi, I am running into this issue /usr/share/lmod/lmod/init/bash: line 163: conda: command not found /

11/21/22

11/4/22

sparseToDense.py error

Hi When I use sparseToDense.py to convert HiC-Pro output into dense format: python 00.sparseToDense.

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sparseToDense.py error

Hi When I use sparseToDense.py to convert HiC-Pro output into dense format: python 00.sparseToDense.

11/4/22

Juan A Rodriguez, nservant5

10/14/22

HiCPro output format?

Oh, I see. At the moment it's running fine... but will take that into consideration for the

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HiCPro output format?

Oh, I see. At the moment it's running fine... but will take that into consideration for the

10/14/22

Clifford Rostomily, nservant2

10/5/22

What do Pairs_with_singleton refer to in the statistics?

Hi, Singleton means that you only have one of the two reads which is aligned on the reference genome.

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What do Pairs_with_singleton refer to in the statistics?

Hi, Singleton means that you only have one of the two reads which is aligned on the reference genome.

10/5/22

Jaclyn Andricovich

9/25/22

Docker/Java advice for utils?

Hello, I have been running the HiC-Pro pipeline in Docker with great success. Thank you Nicolas

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Docker/Java advice for utils?

Hello, I have been running the HiC-Pro pipeline in Docker with great success. Thank you Nicolas

9/25/22

Peter Kim, nservant3

9/12/22

inquiries on fragment size distribution

Hi Nicolas, Thank you for your answer! As far as I know, yes. The length of fragment in HICUP also

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inquiries on fragment size distribution

Hi Nicolas, Thank you for your answer! As far as I know, yes. The length of fragment in HICUP also

9/12/22

zhenzhen...@gmail.com, nservant3

9/11/22

Hi Nicolas, Thanks so much for your kind reply.I am biological background and have little knowledge

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Hi Nicolas, Thanks so much for your kind reply.I am biological background and have little knowledge

9/11/22

xianqiang wang, nservant2

9/10/22

Bowtie stopped when mapping the last set of files

Hi Do you have any specific message ? could it be a time out issue on your server ? N On Monday, 1

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Bowtie stopped when mapping the last set of files

Hi Do you have any specific message ? could it be a time out issue on your server ? N On Monday, 1

9/10/22

Gang Li, nservant8

8/30/22

HiC-Pro Running Error

Hi Nicolas, Have you got the chance to take a look at the downsampled data? I recently tried to run

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HiC-Pro Running Error

Hi Nicolas, Have you got the chance to take a look at the downsampled data? I recently tried to run

8/30/22

kaivalya shevade, nservant2

7/29/22

Error during mapping

Hi Kaivalya, This is not related to HiC-Pro. Samtools is not correctly installed on your system.

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Error during mapping

Hi Kaivalya, This is not related to HiC-Pro. Samtools is not correctly installed on your system.

7/29/22

goek...@googlemail.com, … nservant3

7/29/22

Differential interaction analysis

Thanks @Herman for your contribution ! @Deniz, it theory, you should have all counts table in the

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Differential interaction analysis

Thanks @Herman for your contribution ! @Deniz, it theory, you should have all counts table in the

7/29/22

7/4/22

HiC-Pro error / make warning when using Singularity (make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.)

Hello, I'm trying to use HiC-Pro through Singularity. I created my own Singularity image using

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HiC-Pro error / make warning when using Singularity (make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.)

Hello, I'm trying to use HiC-Pro through Singularity. I created my own Singularity image using

7/4/22

kaivalya shevade, nservant3

6/29/22

failed to create symbolic link

Thanks for the reply. I actually figured it was an error in the config file. I had added the path to

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failed to create symbolic link

Thanks for the reply. I actually figured it was an error in the config file. I had added the path to

6/29/22

Nadya Fursova, nservant2

6/29/22

Using HiC-Pro to analyze Micro-C data

Hi Nadya, Did you fix your issue ? N On Friday, 7 January 2022 at 04:35:20 UTC+1 nfurso...@gmail.com

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Using HiC-Pro to analyze Micro-C data

Hi Nadya, Did you fix your issue ? N On Friday, 7 January 2022 at 04:35:20 UTC+1 nfurso...@gmail.com

6/29/22

Robert King, … nservant7

6/29/22

Arima v2.0 kit cuts digest_genome.py script

Hi Konstantin, Yes, please look at https://github.com/nservant/HiC-Pro/blob/master/doc/FAQ.md Best On

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Arima v2.0 kit cuts digest_genome.py script

Hi Konstantin, Yes, please look at https://github.com/nservant/HiC-Pro/blob/master/doc/FAQ.md Best On

6/29/22

Jie Liu, nservant2

6/29/22

Can I provide my snp_VCF file instead of generating it from extract_snps.py?

Hi, Sorry for the delay. Yes I think it should work. So finally, did you try it ? N On Sunday, 6

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Can I provide my snp_VCF file instead of generating it from extract_snps.py?

Hi, Sorry for the delay. Yes I think it should work. So finally, did you try it ? N On Sunday, 6

6/29/22

2/16/22

make: *** [bowtie_pairing] Error 1

Dear all, I was running the HiC-Pro pipeline and received this error"/scripts//Makefile:141:

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make: *** [bowtie_pairing] Error 1

Dear all, I was running the HiC-Pro pipeline and received this error"/scripts//Makefile:141:

2/16/22

1/8/22

HiC-Protojuice box error, hic format file cannot do loop calling

Dear all! I met a problem when I tried to convert the HiC output to juicebox input to call loops on

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HiC-Protojuice box error, hic format file cannot do loop calling

Dear all! I met a problem when I tried to convert the HiC output to juicebox input to call loops on

1/8/22

12/15/21

Problem converting allValidPairs files to .hic using hicpro2juicebox.sh

Edit: I noticed that the restriction fragment file I obtained was missing chrX and chrY. I am now

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Problem converting allValidPairs files to .hic using hicpro2juicebox.sh

Edit: I noticed that the restriction fragment file I obtained was missing chrX and chrY. I am now

12/15/21

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