juicer pre and addnorm

cqhon...@gmail.com

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Jan 11, 2021, 5:34:21 AM1/11/21

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Hi,

In "https://github.com/aidenlab/juicer/blob/master/CPU/juicer.sh", there is a command:

${juiceDir}/scripts/common/juicer_tools pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath

Then I searched "pre" in "https://github.com/aidenlab/juicer/wiki/Pre" and found that it has a parameter "-n", which means "Don't normalize the matrices". However, in the command above, there is no "-n". What is the output .hic file after running the command? Is it the raw Hi-C contacts (no normalization) or the normalized contacts?

And I also noticed a "-k" in "https://github.com/aidenlab/juicer/wiki/Pre", is there a default value for "-k" (e.g. KR normalization)?

Thanks in advance.

Qin

Qin Cao

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Jan 13, 2021, 3:15:47 AM1/13/21

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Dear Neva,

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Best Regards,

CAO Qin

Lisa Young

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Jan 13, 2021, 3:16:12 AM1/13/21

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Sincerely,

Lisa Young

Neva Durand

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Jan 13, 2021, 9:04:34 AM1/13/21

to Qin Cao, 3D Genomics

Calculating contact matrices and calculating norm vectors is two separate steps but both happen by default when you call Pre.

Sometimes people don't want norm vectors so there's an option for that.

The hic file contains both non-normalized values and normalized values. You can see this by loading a hic file into Juicebox and clicking on different normalizations.

The default normalizations calculated are KR, VC, SCALE. If you only wanted to calculate one, you can send that in with the -k flag.

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Neva Cherniavsky Durand, Ph.D. | she, her, hers

Assistant Professor | Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org