3D/4D modeling form Hi-C data
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**CustardPy** has an advanced command for 3D modeling and 4D simulatuion using the Hi-C matrix.
run-pastis.sh
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``run-pastis.sh`` implements `PASTIS `_ and estimates 3D models from the Hi-C contact matrix.
.. code-block:: bash
odir=JuicerResults/Sample
# genomic region to be simulated
chr=chr21
s=24000000
e=32000000
resolution=100000
norm=SCALE # normalization type
run-pastis.sh $odir $chr $s $e $resolution $norm
phic_processing
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``phic_processing`` implements `PHi-C2 `_ and generates biophysical polymer model.
.. code-block:: bash
hic=$odir/aligned/inter_30.hic
odir=phic_result
# genomic region to be simulated
chr=chr21
start=24000000
end=32000000
resolution=100000
norm=SCALE # normalization type
phic_processing $odir $hic $chr $start $end $resolution $norm