Some general questions about juicer

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Luciana Ant

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May 5, 2021, 4:03:33 PM5/5/21
to 3D Genomics
Hello everyone, 
I am really new to these types of platforms, so i'm a bit confused about the requirements. I need to transform a fastq file to a hic one, can i run the pipeline in my cpu or do i need to use a cluster? How much ram do you think it requires? To do this i only need to use the juicer.sh command, right? Not any juicer tools

Thank you in advance,
Luciana

Neva Durand

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May 6, 2021, 10:20:05 AM5/6/21
to Luciana Ant, 3D Genomics
Hello Luciana,

Cluster vs CPU depends on how many reads you have. With deep maps, CPU will take a very long time / is not worth it. RAM requirements will also depend on how many reads. There are also cloud based Juicers, on AWS and a new one in beta testing from the ENCODE DCC.


juicer_tools is a part of the Juicer pipeline and must be run to convert the pairwise contacts to the .hic file

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Neva Cherniavsky Durand, Ph.D. | she, her, hers
Assistant Professor |  Molecular and Human Genetics
Aiden Lab | Baylor College of Medicine
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