Juicer -x exclude fragment file from hic creation. What's the diference?

[ricardogue...@gmail.com]

Hello,

I would like to understand the difference between using -x or not in the creation of hic files with Juicer, besides the speed. Will the Juicebox maps look any different between hic files created including or excluding the fragment file?

Kind regards,

Ricardo

[Neva Durand]

Hello,

The maps will not look any different. Fragment-delimited maps are additional contact maps that are delimited by fragments instead of by base pair resolution. So instead of 100Kb e.g., you can have a map binned every 10 fragments. You can change to fragment delimited maps by clicking the resolution slider:

https://github.com/aidenlab/Juicebox/wiki/Exploring-the-Data#resolution-slider

If you do not store fragment delimited maps, you lose this capability. Otherwise everything remains the same.

Note that we will soon be making the default be to exclude fragment delimited maps, since this doesn't seem to be a capability that most research groups utilize.

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org