#############################################################Genome perl bow2bed.pl YBX1Y_4su_3G.bowtie YBX1Y_4su_3Ggenome sort -k1,1 -k2,2n YBX1Y_4su_3Ggenome.bed > YBX1Y_4su_3Ggenomesort.bed perl filterPCR2.pl YBX1Y_4su_3Ggenomesort.bed YBX1Y_4su_3GgenomesortPCRfilt perl T_C.pl YBX1Y_4su_3GgenomesortPCRfilt.bed YBX1Y_4su_3GgenomesortPCRfiltT_C genomeCoverageBed -bg -strand - -i YBX1Y_4su_3GgenomesortPCRfilt.bed -g human.hg19.genome > YBX1Y_4su_3GgenomesortPCRfiltcovminus.bg genomeCoverageBed -bg -strand + -i YBX1Y_4su_3GgenomesortPCRfilt.bed -g human.hg19.genome > YBX1Y_4su_3GgenomesortPCRfiltcovplus.bg awk -v th=5 -v strand="-" -f bedgraph2bed2b.awk YBX1Y_4su_3GgenomesortPCRfiltcovminus.bg > YBX1Y_4su_3Ggenomesortover5.bed awk -v th=5 -v strand="+" -f bedgraph2bed2b.awk YBX1Y_4su_3GgenomesortPCRfiltcovplus.bg >> YBX1Y_4su_3Ggenomesortover5.bed genomeCoverageBed -bg -strand - -i YBX1Y_4su_3GgenomesortPCRfiltT_C.bed -g human.hg19.genome > YBX1Y_4su_3GgenomesortPCRfiltT_Cminus.bg genomeCoverageBed -bg -strand + -i YBX1Y_4su_3GgenomesortPCRfiltT_C.bed -g human.hg19.genome > YBX1Y_4su_3GgenomesortPCRfiltT_Cplus.bg awk -v th=1 -v strand="-" -f bedgraph2bed2b.awk YBX1Y_4su_3GgenomesortPCRfiltT_Cminus.bg > YBX1Y_4su_3GgenomesortoverTC.bed awk -v th=1 -v strand="+" -f bedgraph2bed2b.awk YBX1Y_4su_3GgenomesortPCRfiltT_Cplus.bg >> YBX1Y_4su_3GgenomesortoverTC.bed intersectBed -a YBX1Y_4su_3Ggenomesortover5.bed -b YBX1Y_4su_3GgenomesortoverTC.bed -s -wa -wb > YBX1Y_4su_3Ggenomeover5-TC.bed perl avonegeneb2b.pl YBX1Y_4su_3Ggenomeover5-TC.bed YBX1Y_4su_3Ggenomeover5-TCav perl cutdoubleav.pl YBX1Y_4su_3Ggenomeover5-TCav.bed YBX1Y_4su_3Ggenomeover5-TCavC perl ratioT_C.pl YBX1Y_4su_3Ggenomeover5-TCavC.bed YBX1Y_4su_3Ggenomeover5-TCavCratio perl extractmpT_C.pl YBX1Y_4su_3Ggenomeover5-TC.bed YBX1Y_4su_3Ggenomeover5-mpTC ###############################################################Trans perl find_Tcoordinates2.pl transcripts.fa YBX1Y_4su_3Tb.bowtie YBX1Y_4su_3Ttrans perl fixreads1.pl YBX1Y_4su_3Ttrans.bed YBX1Y_4su_3transC perl fixreads.pl YBX1Y_4su_3Ttrans.bed YBX1Y_4su_3transCc sort -k1,1 -k2,2n YBX1Y_4su_3transCc.bed > YBX1Y_4su_3transsort.bed perl filterPCR.pl YBX1Y_4su_3transsort.bed YBX1Y_4su_3transsortPCRfilt perl T_C.pl YBX1Y_4su_3transsortPCRfilt.bed YBX1Y_4su_3transsortPCRfilt_C genomeCoverageBed -bg -strand - -i YBX1Y_4su_3transsortPCRfilt.bed -g human.hg19.genome > YBX1Y_4su_3transsortPCRfiltcovminus.bg genomeCoverageBed -bg -strand + -i YBX1Y_4su_3transsortPCRfilt.bed -g human.hg19.genome > YBX1Y_4su_3transsortPCRfiltcovplus.bg awk -v th=5 -v strand="-" -f bedgraph2bed2b.awk YBX1Y_4su_3transsortPCRfiltcovminus.bg > YBX1Y_4su_3transsortover5.bed awk -v th=5 -v strand="+" -f bedgraph2bed2b.awk YBX1Y_4su_3transsortPCRfiltcovplus.bg >> YBX1Y_4su_3transsortover5.bed genomeCoverageBed -bg -strand - -i YBX1Y_4su_3transsortPCRfilt_C.bed -g human.hg19.genome > YBX1Y_4su_3transsortPCRfilt_Cminus.bg genomeCoverageBed -bg -strand + -i YBX1Y_4su_3transsortPCRfilt_C.bed -g human.hg19.genome > YBX1Y_4su_3transsortPCRfilt_Cplus.bg awk -v th=1 -v strand="-" -f bedgraph2bed2b.awk YBX1Y_4su_3transsortPCRfilt_Cminus.bg > YBX1Y_4su_3transsortoverTC.bed awk -v th=1 -v strand="+" -f bedgraph2bed2b.awk YBX1Y_4su_3transsortPCRfilt_Cplus.bg >> YBX1Y_4su_3transsortoverTC.bed intersectBed -a YBX1Y_4su_3transsortover5.bed -b YBX1Y_4su_3transsortoverTC.bed -s -wa -wb > YBX1Y_4su_3transsortover5-TC.bed perl avonegeneb2b.pl YBX1Y_4su_3transsortover5-TC.bed YBX1Y_4su_3transsortover5-TCav perl cutdoubleav.pl YBX1Y_4su_3transsortover5-TCav.bed YBX1Y_4su_3transsortover5-TCavC perl ratioT_C.pl YBX1Y_4su_3transsortover5-TCavC.bed YBX1Y_4su_3transsortover5-TCavCratio perl extractmpT_C.pl YBX1Y_4su_3transsortover5-TC.bed YBX1Y_4su_3transsortover5-mpTC