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