# chaos.juicer
The repository was originally forked from aidenlab/juicer.
the juicer V2 were modified to adapted to SUSTech cluster.

## usage
The juicer.sh was separated into 3 steps: 

hic_slice

hic_align

hic_generation.

The usage of the modified pipeline are as folllows:

./hic_slice.sh hic_info.sh 1

There are 2 parameters for it, 

hic_info.sh contains the Hi-C experiment info, and the name could be changed.

1 means that the generated bash files will be automatically uploded to the server, and will be delated.

if you want to have a final check, change it to 0.

it’s the same for another 2 steps

## juicer_local
It's still under development.

juicer_local merged the above 3 steps into 1 file, and could be executed on local machine, please be noted that the align step need quite a long time and large memory

the use of it is the same with the separate one except that it won't generate another .sh file 

## using KR normalization
if you are going to use KR normalization, 

the latest juicer_tools version is 2.14.0, 

and you need to use -k to include KR when using pre

