lh3 / hickit

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
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Gaining intuition/information about script key word arguments. #35

Open Xparx opened 1 year ago

Xparx commented 1 year ago

Hello,

I'm trying to understand how hickit is used best and need to get some insight into what parameters affect what. Specifically I'm trying to decode and understand the binning and contact arguments from this command line

hickit -i imput.pairs -Sr1m -c1 -r10m -c5 -o imput.flt.pairs

to me it looks like some arguments are repeated and changed. Where can I read up on how this works?

The same question for the following command

hickit -i imput.flt.pairs -b4m -b1m -b200k -O coarse.3dg

Many thanks.