./mergeMyPar.sh sh-clusters-0hrep1.txt3 ./mergeMyPar.sh sh-clusters-0hrep2.txt3 ./mergeMyPar.sh sh-clusters-0hrep3.txt3 ./mergeMyPar.sh sh-clusters-2hrep1.txt3 ./mergeMyPar.sh sh-clusters-2hrep2.txt3 ./mergeMyPar.sh sh-clusters-2hrep3.txt3 ./mergeMyPar.sh sh-clusters-6hrep1.txt3 ./mergeMyPar.sh sh-clusters-6hrep2.txt3 ./mergeMyPar.sh sh-clusters-6hrep3.txt3 ./mergeMyPar.sh sh-clusters-IGG.txt3 ./mergeMyPar.sh sh-clusters-IL4.txt3 ./mergeMyPar.sh sh-clusters-IFN.txt2 ./mergeMyPar.sh sh-distributions-0hrep1.txt3 ./mergeMyPar.sh sh-distributions-0hrep2.txt3 ./mergeMyPar.sh sh-distributions-0hrep3.txt3 ./mergeMyPar.sh sh-distributions-2hrep1.txt3 ./mergeMyPar.sh sh-distributions-2hrep2.txt3 ./mergeMyPar.sh sh-distributions-2hrep3.txt3 ./mergeMyPar.sh sh-distributions-6hrep1.txt3 ./mergeMyPar.sh sh-distributions-6hrep2.txt3 ./mergeMyPar.sh sh-distributions-6hrep3.txt3 ./mergeMyPar.sh sh-distributions-IGG.txt3 ./mergeMyPar.sh sh-distributions-IL4.txt3 ./mergeMyPar.sh sh-distributions-IFN.txt2 ./mergeMyPar.sh sh-groups-0hrep1.txt3 ./mergeMyPar.sh sh-groups-0hrep2.txt3 ./mergeMyPar.sh sh-groups-0hrep3.txt3 ./mergeMyPar.sh sh-groups-2hrep1.txt3 ./mergeMyPar.sh sh-groups-2hrep2.txt3 ./mergeMyPar.sh sh-groups-2hrep3.txt3 ./mergeMyPar.sh sh-groups-6hrep1.txt3 ./mergeMyPar.sh sh-groups-6hrep2.txt3 ./mergeMyPar.sh sh-groups-6hrep3.txt3 ./mergeMyPar.sh sh-groups-IGG.txt3 ./mergeMyPar.sh sh-groups-IL4.txt3 ./mergeMyPar.sh sh-groups-IFN.txt2 mv sh-groups-IFN.txt2.csv sh-groups-IFN.txt3.csv mv sh-distributions-IFN.txt2.csv sh-distributions-IFN.txt3.csv mv sh-clusters-IFN.txt2.csv sh-clusters-IFN.txt3.csv # paralyzer to bed for i in sh-clusters*txt3.csv do echo $i awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2bed.awk $i > $i.bed done # keep scores >= 0.9 for i in sh-clusters-*txt3.csv.bed do wc $i cat $i | awk -v th=0.9 -f ../filter-pa-bed.awk > $i.flt wc $i.flt done #remove IGG regions for i in sh-clusters-*txt3.csv.bed.flt do wc $i bedtools intersect -a $i -b sh-clusters-IGG.txt3.csv.bed.flt -v |sort -k1,1 -k2,2n > $i.noIGG wc !$ done # strand stats for i in sh-clusters-*txt3.csv.bed.flt.noIGG do echo $i awk -f ../strandStats1.awk $i done awk -f ../strandStats1.awk sh-clusters-IGG.txt3.csv.bed.flt # separate plus strand results for i in sh-clusters-*txt3.csv.bed.flt.noIGG do wc $i awk -f ../filterPlusStrand.awk $i > $i.plus wc !$ done awk -f ../filterPlusStrand.awk sh-clusters-IGG.txt3.csv.bed.flt > sh-clusters-IGG.txt3.csv.bed.flt.plus # merge strands for i in sh-clusters-*txt3.csv.bed.flt.noIGG do wc $i cat $i | bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - > $i.unstranded wc !$ done wc sh-clusters-IGG.txt3.csv.bed.flt #88624 531744 9899764 sh-clusters-IGG.txt3.csv.bed.flt cat sh-clusters-IGG.txt3.csv.bed.flt|sort -k1,1 -k2,2n |bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - >sh-clusters-IGG.txt3.csv.bed.flt.unstranded wc sh-clusters-IGG.txt3.csv.bed.flt.unstranded #86814 434070 9671361 sh-clusters-IGG.txt3.csv.bed.flt.unstranded #add annotation for i in sh-clusters-*unstranded do echo $i awk -f ../pa2annotate1.awk $i |sort -k1,1 -k2,2n > $i".anno.csv" done cd res/per_sample_plus/ for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/*plus do echo $i awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk $i |sort -k1,1 -k4,4 -k2,2n -k5,5n > $i.anno.csv ln -s !$ done ls s*0h* | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/intersect_modeLocation1.awk > 0h_commonModelocation_GT1.txt ls s*2h* | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/intersect_modeLocation1.awk > 2h_commonModelocation_GT1.txt ls s*6h* | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/intersect_modeLocation1.awk > 6h_commonModelocation_GT1.txt cd ../.. cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/per_sample_plus_sensitive # region stats for i in sh-clusters-*unstranded do echo $i awk -f ../pa2stats1.awk $i done cd res/per_sample/ for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b*anno.csv do ln -s $i done cd ../.. #cluster region union cat sh-clusters-0hrep1.txt3.csv.bed.flt.noIGG.unstranded sh-clusters-0hrep2.txt3.csv.bed.flt.noIGG.unstranded sh-clusters-0hrep3.txt3.csv.bed.flt.noIGG.unstranded| sort -k1,1 -k2,2n | bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - > sh-clusters-0h.flt.noIGG.unstranded.merged.bed 506627 2533135 64580156 sh-clusters-0h.flt.noIGG.unstranded.merged.bed cat sh-clusters-2hrep1.txt3.csv.bed.flt.noIGG.unstranded sh-clusters-2hrep2.txt3.csv.bed.flt.noIGG.unstranded sh-clusters-2hrep3.txt3.csv.bed.flt.noIGG.unstranded| sort -k1,1 -k2,2n | bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - > sh-clusters-2h.flt.noIGG.unstranded.merged.bed 437476 2187380 54900609 sh-clusters-2h.flt.noIGG.unstranded.merged.bed cat sh-clusters-6hrep1.txt3.csv.bed.flt.noIGG.unstranded sh-clusters-6hrep2.txt3.csv.bed.flt.noIGG.unstranded sh-clusters-6hrep3.txt3.csv.bed.flt.noIGG.unstranded| sort -k1,1 -k2,2n | bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - > sh-clusters-6h.flt.noIGG.unstranded.merged.bed 498294 2491470 64601488 sh-clusters-6h.flt.noIGG.unstranded.merged.bed #cluster region intersection bedtools intersect -a sh-clusters-0hrep1.txt3.csv.bed.flt.noIGG.unstranded -b sh-clusters-0hrep2.txt3.csv.bed.flt.noIGG.unstranded -wa -wb -sorted > sh-clusters-0h.flt.noIGG.unstranded.intersection12.bed1 bedtools intersect -a sh-clusters-0hrep3.txt3.csv.bed.flt.noIGG.unstranded -b sh-clusters-0h.flt.noIGG.unstranded.intersection12.bed1 -wa -wb -sorted > sh-clusters-0h.flt.noIGG.unstranded.intersection.bed wc sh-clusters-0h.flt.noIGG.unstranded.intersection.bed 3957 59355 1455714 sh-clusters-0h.flt.noIGG.unstranded.intersection.bed bedtools intersect -a sh-clusters-2hrep1.txt3.csv.bed.flt.noIGG.unstranded -b sh-clusters-2hrep2.txt3.csv.bed.flt.noIGG.unstranded -wa -wb -sorted > sh-clusters-2h.flt.noIGG.unstranded.intersection12.bed1 bedtools intersect -a sh-clusters-2hrep3.txt3.csv.bed.flt.noIGG.unstranded -b sh-clusters-2h.flt.noIGG.unstranded.intersection12.bed1 -wa -wb -sorted > sh-clusters-2h.flt.noIGG.unstranded.intersection.bed wc sh-clusters-2h.flt.noIGG.unstranded.intersection.bed 3851 57765 1400223 sh-clusters-2h.flt.noIGG.unstranded.intersection.bed bedtools intersect -a sh-clusters-6hrep1.txt3.csv.bed.flt.noIGG.unstranded -b sh-clusters-6hrep2.txt3.csv.bed.flt.noIGG.unstranded -wa -wb -sorted > sh-clusters-6h.flt.noIGG.unstranded.intersection12.bed1 bedtools intersect -a sh-clusters-6hrep3.txt3.csv.bed.flt.noIGG.unstranded -b sh-clusters-6h.flt.noIGG.unstranded.intersection12.bed1 -wa -wb -sorted > sh-clusters-6h.flt.noIGG.unstranded.intersection.bed wc sh-clusters-6h.flt.noIGG.unstranded.intersection.bed 6482 97230 2412958 sh-clusters-6h.flt.noIGG.unstranded.intersection.bed