Applicability with Omni-C?

Question

Applicability with Omni-C?

Opened this issue a year ago · 4 comments

Hello,

EndHiC requires HiC-Pro outputs. And HiC-Pro inputs require a bed file with all restriction cut sites in a given genome. As it stands, it is not possible to use HiC-Pro outputs since by definition Omni-C does not have any restriction sites.

Is there an approach to use EndHiC with Omni-C data I am not considering?

Thank you,
Sam

Answer 1 · 2023-07-21T22:36:53.000Z

You can calcualte the Hi-C link number for each bin in all the contigs by yourself. EndHiC just need this matrix data as input. ***@***.*** From: Sam Talbot Date: 2023-07-22 05:15 To: fanagislab/EndHiC CC: Subscribed Subject: [fanagislab/EndHiC] Applicability with Omni-C? (Issue #5) Hello, EndHiC requires HiC-Pro outputs. And HiC-Pro inputs require a bed file with all restriction cut sites in a given genome. As it stands, it is not possible to use HiC-Pro outputs since by definition Omni-C does not have any restriction sites. Is there an approach to use EndHiC with Omni-C data I am not considering? Thank you, Sam — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

Answer 2 · 2023-10-03T07:25:05.000Z

@fanagislab Hi. I am also working with OmniC data and interested to evaluate EndHiC. As you mentioned

You can calcualte the Hi-C link number for each bin in all the contigs by yourself. EndHiC just need this matrix data as input.

Could you help on how to generate this matrix? Thank you

Answer 3 · 2023-10-09T00:30:51.000Z

Please try HiC-pro. ***@***.*** From: LHG-GG Date: 2023-10-03 15:25 To: fanagislab/EndHiC CC: fanwei; Mention Subject: Re: [fanagislab/EndHiC] Applicability with Omni-C? (Issue #5) @fanagislab Hi. I am also working with OmniC data and interested to evaluate EndHiC. As you mentioned You can calcualte the Hi-C link number for each bin in all the contigs by yourself. EndHiC just need this matrix data as input. Could you help on how to generate this matrix? Thank you — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

Answer 4 · 2024-02-08T08:40:20.000Z

We've been trying it with Omni-C and have promising results.
Starting with the L1.mapped.pairs file as generated following Dovetail instructions you can do this (hicexplorer v3.7.3 needed):

source activate hicexplorer

bgzip L1.mapped.pairs
pairix L1.mapped.pairs.gz

cooler cload pairix -p 16 ref.genome:100000 L1.mapped.pairs.gz L1.mapped.pairs.100000.cool

hicConvertFormat --matrices L1.mapped.pairs.100000.cool --outFileName L1.mapped.pairs.100000.hicpro --inputFormat cool --outputFormat hicpro --bedFileHicpro L1.mapped.pairs.100000.hicpro.bed

hicConvertFormat --matrices L1.mapped.pairs.100000.cool --outFileName L1.mapped.pairs.100000.h5 --inputFormat cool --outputFormat h5

hicCorrectMatrix diagnostic_plot --matrix L1.mapped.pairs.100000.h5 -o file.png

hicCorrectMatrix correct --matrix L1.mapped.pairs.100000.h5 --filterThreshold -3 3 --correctionMethod ICE --outFileName L1.mapped.pairs.100000.ICE.h5

cp L1.mapped.pairs.100000.hicpro.bed L1.mapped.pairs.100000.hicpro.copy.bed

hicConvertFormat --matrices L1.mapped.pairs.100000.ICE.h5 --outFileName L1.mapped.pairs.100000.hicpro.ICE --inputFormat h5 --outputFormat hicpro --bedFileHicpro L1.mapped.pairs.100000.hicpro.bed

#Renaming is needed for the files to be read properly

mv L1.mapped.pairs.100000.hicpro.ICE BraHiC_100000_iced.matrix
mv L1.mapped.pairs.100000.hicpro BraHiC_100000.matrix
mv L1.mapped.pairs.100000.hicpro.bed BraHiC_100000_abs.bed