Using Juicer with Omni-C data

[David]

Hello everyone,

I am trying to use Juicer to scaffold and visualize my genome using Omni-C data. 

This is the command I am using:

~/juicer/scripts/juicer.sh -D ~/juicer/ -z ../references/Assembly_RP3.fasta -t 30 -s none

This creates an error: ***! You must define a chrom.sizes file via the "-p" flag that delineates the lengths of the chromosomes in the genome at ../references/CYCOLD_RP3.fasta; you may use "-p hg19" or other standard genomes

I am not sure why this is happening, since I am using the -s flag and should therefore not require this file. 

Does someone have an idea on why this is happening? 

[Neva Durand]

-s none refers to the restriction enzyme, not the genome.

For assembly purposes you don't need to create the hic file, so add the flags "-e" (for early exit) and "-p hg19" (to get rid of that error message; it won't be used if early exit).

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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

[David]

Thank you for your quick answer! I suspected as much, but since I am having problems with my results I thought maybe this could affect them as well.