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Make_WholeGenome_Matrix.sh
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Make_WholeGenome_Matrix.sh
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chrSizeFile="/mnt/extraids/OceanStor-SysCmn-1/rcalandrelli/Project____InterChrom/Data/4DN_files_reference/4DNFI823LSII.hg38.mainonly.chrom.sizes"
ChrList="chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY"
### Contact maps at 200 kb
# HUVEC replicate 1
InputFileBase="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/HUVEC_20180613_library2_control_igm/01_04____Split_iMARGI_ChrBrChr/Single_HUVECcontrol2."
OutputPath="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/HUVEC_20180613_library2_control_igm/HUVECcontrol__Matrix__Resolution200000/"
InputFileBase="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/HUVEC_H_T3d_P6_igm____R2filtered/01_04____Split_iMARGI_ChrBrChr/Single_HUVECcontrol2."
OutputPath="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/HUVEC_H_T3d_P6_igm____R2filtered/HUVECcontrol__Matrix__Resolution200000/"
InputFileBase="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/HUVEC_H_T7d_P7_igm____R2filtered/01_04____Split_iMARGI_ChrBrChr/Single_HUVECcontrol2."
OutputPath="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/HUVEC_H_T7d_P7_igm____R2filtered/HUVECcontrol__Matrix__Resolution200000/"
# HUVEC replicate 2
InputFileBase="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/replicate_2/HUVEC_control_igm____R2filtered/01_04____Split_iMARGI_ChrBrChr/Single_HUVECcontrol2."
OutputPath="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/replicate_2/HUVEC_control_igm____R2filtered/HUVECcontrol__Matrix__Resolution200000/"
InputFileBase="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/replicate_2/HUVEC_T7d_P7_igm____R2filtered/01_04____Split_iMARGI_ChrBrChr/Single_HUVECcontrol2."
OutputPath="/mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/replicate_2/HUVEC_T7d_P7_igm____R2filtered/HUVECcontrol__Matrix__Resolution200000/"
# To be executed per each sample
Resolution=200000
for chrA in ${ChrList}
do
for chrB in ${ChrList}
do
python2.7 /mnt/extraids/OceanStor-SysCmn-2/rcalandrelli/MARGI/replicate_2/RNAvsDNA_matrix_between_a_pair_of_chromosomes.PY27.py -i ${InputFileBase}${chrA}_${chrB}.bedpe -o ${OutputPath} --chrSize ${chrSizeFile} -c 200000 -r ${Resolution} --rna_chr ${chrA} --dna_chr ${chrB}
done
done