Fit-Hi-C

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Welcome to the new Fit-Hi-C forum. Any and all questions, discussion, or bug reports may be added here.

Happy analysis!

Note: Before posting, check the Github 'issues' page to see if your question has already been addressed.

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hengkuan li

6/3/25

Issues regarding the use of merged-filter.sh

Hi, May I ask if it is necessary to use merge-filter.sh to merge nearby significant interactions and

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Issues regarding the use of merged-filter.sh

Hi, May I ask if it is necessary to use merge-filter.sh to merge nearby significant interactions and

6/3/25

Colin Kern, … Ferhat Ay4

4/10/25

Problem using HiCKRy.py to generate bias files

Hi, HICKRy.py also has some issues for some chromosomes. Using VC normalization from Juicer is

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Problem using HiCKRy.py to generate bias files

Hi, HICKRy.py also has some issues for some chromosomes. Using VC normalization from Juicer is

4/10/25

Tuba

12/17/24

Issue with Mustache for Interchromosomal Interactions

I'm running Mustache for interchromosomal interactions and encountered an error : Normalizing

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Issue with Mustache for Interchromosomal Interactions

I'm running Mustache for interchromosomal interactions and encountered an error : Normalizing

12/17/24

Gambling News

2/15/24

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mars4d🎉adalah raja bandot terpercaya di Indonesia yang menyediakan hut4d🌠 ribuan link alternatif

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cukong88💰⛏Situs Platform Gaming Judi Slot Online Gacor 🟣💰kencana88

mars4d🎉adalah raja bandot terpercaya di Indonesia yang menyediakan hut4d🌠 ribuan link alternatif

2/15/24

Savio Chow

2/28/23

All GM12878 p-values and q-values for intra-chromosomal interactions have nan value

Hi, I downloaded the GM12878 .hic file from 4DN (4DNFI1UEG1HD.hic). I used juicer dump for each

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All GM12878 p-values and q-values for intra-chromosomal interactions have nan value

Hi, I downloaded the GM12878 .hic file from 4DN (4DNFI1UEG1HD.hic). I used juicer dump for each

2/28/23

kaivalya shevade, Ferhat Ay2

2/28/23

Question about createFitHiCFragments-fixedsize.py

Hi, Both are the correct format, the two fields that matter the most are 1st and 3rd and in both

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Question about createFitHiCFragments-fixedsize.py

Hi, Both are the correct format, the two fields that matter the most are 1st and 3rd and in both

2/28/23

kaivalya shevade

2/14/23

Problems with the merge-filter.sh script

Hi, I was trying to run Fit-Hi-C on a HiC dataset. To begin with I only decided to run Fit-Hi-C on

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Problems with the merge-filter.sh script

Hi, I was trying to run Fit-Hi-C on a HiC dataset. To begin with I only decided to run Fit-Hi-C on

2/14/23

Elena Del Pup, Ferhat Ay5

12/13/22

Binarizing significant/insignificant interactions

Your BH critical value can't be 0.99 etc. The standard thresholds people would use are 0.01 or

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Binarizing significant/insignificant interactions

Your BH critical value can't be 0.99 etc. The standard thresholds people would use are 0.01 or

12/13/22

Daiane Hemerich, Ferhat Ay2

8/19/22

FitHiC2 with replicates

You can either combine (simple concatenation) the two validPairs files before creating contact maps

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FitHiC2 with replicates

You can either combine (simple concatenation) the two validPairs files before creating contact maps

8/19/22

Daiane Hemerich

8/19/22

Key error running HiCKRy.py

Hi, I'd like to run FitHiC2 using a publicly available validPairs file generated from human heart

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Key error running HiCKRy.py

Hi, I'd like to run FitHiC2 using a publicly available validPairs file generated from human heart

8/19/22

PavlaN2

7/14/22

TypeError: can only concatenate str (not "int") to str

Problem solved by removing all fragments with 0 mappability from the mappablity files and those with

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TypeError: can only concatenate str (not "int") to str

Problem solved by removing all fragments with 0 mappability from the mappablity files and those with

7/14/22

shardul kamble

12/24/21

Unable to run the command ./run_tests-cli.sh

I tried to check in the tests folder but there was no file named as run_tests-cli.sh. Instead there

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Unable to run the command ./run_tests-cli.sh

I tried to check in the tests folder but there was no file named as run_tests-cli.sh. Instead there

12/24/21

yang chen

11/16/21

HicPro input for Fit-Hi-C

Hello, I used HiCPro2FitHiC.py to convert the .matrix, _abs.bed and .5000_iced.matrix.biases files

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HicPro input for Fit-Hi-C

Hello, I used HiCPro2FitHiC.py to convert the .matrix, _abs.bed and .5000_iced.matrix.biases files

11/16/21

Mzwanele Ngubo, Ferhat Ay4

8/10/21

Merging inputs of hicpro2fithic.py

You can create a "key" from the ij pair in the matrix file and then read the first file

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Merging inputs of hicpro2fithic.py

You can create a "key" from the ij pair in the matrix file and then read the first file

8/10/21

yinjian...@gmail.com

7/12/21

Why possibleIntraInRangeCount calculated this way

Hi, I am reading the fithic.py script, and find it hard to understand line 622-642, the effect of

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Why possibleIntraInRangeCount calculated this way

Hi, I am reading the fithic.py script, and find it hard to understand line 622-642, the effect of

7/12/21

Chun Su, Ferhat Ay2

6/13/21

compare Hi-C loop calls across multiple cell type

REad count has a quite strong impact on the loop calls. But as your A vs B comparison shows, it is

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compare Hi-C loop calls across multiple cell type

REad count has a quite strong impact on the loop calls. But as your A vs B comparison shows, it is

6/13/21

Gabriel D, Ferhat Ay2

6/13/21

Fit-Hi-C vs. MUSTACHE?

One finds enrichments of interactions wrt global background. The other finds locally maximal pixels/

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Fit-Hi-C vs. MUSTACHE?

One finds enrichments of interactions wrt global background. The other finds locally maximal pixels/

6/13/21

Chun Su, … Kaul, Arya6

4/15/21

will running fithic chromosome by chromosome at 1kb resolution bias the result?

This is very helpful! Thank you both! On Thursday, April 15, 2021 at 11:10:49 AM UTC-4 arya...@g.

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will running fithic chromosome by chromosome at 1kb resolution bias the result?

This is very helpful! Thank you both! On Thursday, April 15, 2021 at 11:10:49 AM UTC-4 arya...@g.

4/15/21

James Smith, Ferhat Ay4

4/12/21

Bias Values are super low. Fithic dumps all bins

It looks ALL good actually. The y-axis in these splines is not the p-value, it is the prior contact

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Bias Values are super low. Fithic dumps all bins

It looks ALL good actually. The y-axis in these splines is not the p-value, it is the prior contact

4/12/21

Colin, Ferhat Ay2

3/11/21

Fragments file format

The file you should be getting should look like this: chr extraField fragmentMid

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Fragments file format

The file you should be getting should look like this: chr extraField fragmentMid

3/11/21

Hiroyuki Kato, Sourya Bhattacharyya3

2/18/21

tabix error to generate WashU browser compatible file

Hi Sourya, Thanks for your reply! Seems that "washu_browser_format.bed.gz" was not prepared

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tabix error to generate WashU browser compatible file

Hi Sourya, Thanks for your reply! Seems that "washu_browser_format.bed.gz" was not prepared

2/18/21

Shanta, Ferhat Ay2

1/28/21

Reason for NA's as p-values and q-values

It is likely because of the bias value filtering filters out more loci at 5kb resolution. For the

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Reason for NA's as p-values and q-values

It is likely because of the bias value filtering filters out more loci at 5kb resolution. For the

1/28/21

Priyatama Pandey

12/11/20

error while running hicpro2fithic.py

Hi, I have result of HicPro and I want to use FitHIC. I used hicpro2fithic.py to create input for the

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error while running hicpro2fithic.py

Hi, I have result of HicPro and I want to use FitHIC. I used hicpro2fithic.py to create input for the

12/11/20

Shanta, Ferhat Ay2

12/8/20

Effect of size of input region on FitHiC outputs

Hi Shanta, Due to several reasons (background estimation and multiple hypothesis testing,

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Effect of size of input region on FitHiC outputs

Hi Shanta, Due to several reasons (background estimation and multiple hypothesis testing,

12/8/20

Guillaume HEGER, Ferhat Ay2

11/24/20

Fit-Hi-C for Region Capture-Hi-C

Hi, yes we have previously applied it to region capture data (Sima et al. Cell 2018). I do not think

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Fit-Hi-C for Region Capture-Hi-C

Hi, yes we have previously applied it to region capture data (Sima et al. Cell 2018). I do not think

11/24/20

Anubhooti -, Ferhat Ay2

11/11/20

Query regarding generating input files

Hi, use for a single chromosome is not an issue at all. I do not know what you mean by contact

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Query regarding generating input files

Hi, use for a single chromosome is not an issue at all. I do not know what you mean by contact

11/11/20

Anna Kononkova, Ferhat Ay2

11/10/20

a 'q-value - distance' plot shows strange result

Hi Anna, This is a great way to look at the results. And you are certainly right in your observation

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a 'q-value - distance' plot shows strange result

Hi Anna, This is a great way to look at the results. And you are certainly right in your observation

11/10/20

Mark Mackiewicz, Kaul, Arya6

10/5/20

Majority of p-values and q-values are either 1 or nan

Hey Mark, Yep, that's correct! You can either generate all 3 files (bias, interaction, fragment)

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Majority of p-values and q-values are either 1 or nan

Hey Mark, Yep, that's correct! You can either generate all 3 files (bias, interaction, fragment)

10/5/20

Daniel Le

8/6/20

MNase-based HiChIP compatible pipeline?

Is FitHIC2 compatible with MNase-based HiChIP protocols? ref: https://dovetailgenomics.com/hichip-

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MNase-based HiChIP compatible pipeline?

Is FitHIC2 compatible with MNase-based HiChIP protocols? ref: https://dovetailgenomics.com/hichip-

8/6/20

ahmed ib, … Kaul, Arya8

7/29/20

Problem in install FitHic - Windows - python 3.7

Thanks for letting us know! I've found quite a bit of people reporting this same error, and am

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discussion

fit-hi-c-r

hicpro2fithic

Problem in install FitHic - Windows - python 3.7

Thanks for letting us know! I've found quite a bit of people reporting this same error, and am

7/29/20