3D/4D modeling form Hi-C data

Contents

8. 3D/4D modeling form Hi-C data#

CustardPy has an advanced command for 3D modeling and 4D simulatuion using the Hi-C matrix.

8.1. run-pastis.sh#

run-pastis.sh implements PASTIS and estimates 3D models from the Hi-C contact matrix.

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

8.2. phic_processing#

phic_processing implements PHi-C2 and generates biophysical polymer model.

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