cd /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/ /home/reczko/bin/faToTwoBit mm9-mRNA-introns1k.fa mm9-mRNA-introns1k.2bit for i in IFN-15mMm.bam for i in 0hrep3-15mMm1kIntron.bam for i in 6hrep3-15mMm1kIntron.bam for i in IGG-15mMm.bam for i in 2hrep?-15mMm1kIntron.bam do echo $i # add MD flags for bowtie format # /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/Mus_musculus.NCBIM37.64-toMM9.max-intron-1k >& /dev/null > foo.bam2 /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/Mus_musculus.NCBIM37.64-toMM9.tr-with-1k-introns.fa >& /dev/null > foo.bam2 samtools view -h foo.bam2 | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk > $i.md.bt mv foo.bam2 $i.md.bam done #uor cd /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k cat 0hrep1-15mMm.bam.md.bt 0hrep2-15mMm.bam.md.bt 0hrep3-15mMm1kIntron.bam.md.bt > 0h-15mMm1kIntron.bam.md.bt wc 0h-15mMm1kIntron.bam.md.bt 222931180 1783449423 29141795018 0h-15mMm1kIntron.bam.md.bt gcc omit-reads.c -lJudy -o omit-reads ./omit-reads /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt # sanity check head -99999 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt | grep "T>C" | wc 13530 108240 1690155 ]0;/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1dreczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d$ head -99999 /data/images/proton/DKlab/mr/parclip/shrimp/0hrep1-15mMm.bam.md.bam.bt | grep "T>C" | wc 14657 117256 1463303 At /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_with_sdev are the clusters with the sdev info added, format: EnsemblID = transcript ID ClusterID = unique ID for the cluster ReadCount = number of reads that overlap the cluster by at least 1 nucleotide ModeLocation = coordinate of the location with the highest signal / (signal + background) value ConversionLocationCount = number of unique location where at least 1 conversion occurred ConversionEventCount = total number of conversions that occurred within the cluster NonConversionEventCount = total number of possible conversion events that did not occur ModeScore = score of the highest signal / (signal + background) value AvgConversionPct = average conversion % of all conversions in the group containing the cluster GroupConversionEventCount = number of all conversions in the group containing the cluster SdevConversionPct = sdev of conversion % of all conversions in the group containing the cluster MaxConversionPct = max. conversion % of all conversions in the group containing the cluster #needed for PARalyzer cs /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k /home/reczko/bin/faToTwoBit mm9-genomic-mRNA.fa mm9-genomic-mRNA.2bit /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/myp-all-1kIntrons2.sh # paralyzer to bed, >= 5 TtoC AND >= 5 reads #/data/images/proton/DKlab/mr/parclip/paralyzer/pa2bed-ge5tc.awk #in: paralyzer format # 1 2 3 4 5 6 7 8 9 10 11 12 #Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ModeScore,ConversionLocationCount,ConversionEventCount,NonConversionEventCount #out: bed format # 1 2 3 4 _ 5 _ 6 _ 7 _ 8 _ 9 _ 10 11 12 # 1 2 3 4 5 6 #Chromosome,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ConversionLocationCount,ConversionEventCount,NonConversionEventCount,ModeScore,Strand for i in sh-clusters-*.txt2-1kIntrons.csv do echo $i awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2bed-gt5tc.awk $i > $i.bed.gt5tc done # /data/images/proton/DKlab/mr/parclip/paralyzer/get-TtoC-conversionPct-noCutoff2.awk adds: ## 1..6(same) AvgConversionPct MaxConversionPct ConversionEventCount SdevConversionPct #to dist # /data/images/proton/DKlab/mr/parclip/paralyzer/pa-dist2bed2.awk #paralyzer+ format #Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,InfoType,AvgConversionPct,MaxConversionPct,ConversionEventCount,SdevConversionPct #1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,10 #out: bed format # 1 2 3 4 _ (7) _ (9) _ (10) 5 _ 6 #Chromosome,ClusterStart,ClusterEnd,ClusterID,AvgConversionPct,ConversionEventCount,SdevConversionPct, MaxConversionPct ,Strand for i in sh-distributions-???*.txt2-1kIntrons.csv do echo $i cat $i| awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/get-TtoC-conversionPct-noCutoff2.awk|awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa-dist2bed2.awk > $i".avg.csv3.bed" done # intersect maxTtoC_gt_0.25 with clusters # (note: /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk adds # AvgConversionPct_ConversionEventCount_SdevConversionPct MaxConversionPct # ) #in: # 1 2 3 4 5 6 7 8 9 10 11 12 #in: ENSMUST00000000254-chr6-+-128884399-128885000 278 324 G5.2_ATTAGTTATTCTATTGGAGTATACAATACTCGAATAGTTCTCAGGCA_275_317_5_96_1643 0.7790820460717197 + ENSMUST00000000254-chr6-+-128884399-128885000 163 374 G5_0.004717_212_0.019691 0.126365 + #input 2 parts #cluster # 1 2 3 4 _ 5 _ 6 _ 7 _ 8 _ 9 _ 10 11 12 # 1 2 3 4 5 6 #Chromosome,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ConversionLocationCount,ConversionEventCount,NonConversionEventCount,ModeScore,Strand #group/dist # 1 2 3 4 _ (7) _ (9) _ (10) 5 6 #Chromosome,ClusterStart,ClusterEnd,ClusterID,AvgConversionPct,ConversionEventCount,SdevConversionPct, MaxConversionPct ,Strand #input all: #cluster # 1 2 3 4 _ 5 _ 6 _ 7 _ 8 _ 9 _ 10 11 12 # 1 2 3 4 5 6 #Chromosome,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ConversionLocationCount,ConversionEventCountC,NonConversionEventCount,ModeScore,Strand #group/dist # 7 8 9 10 11 12 #Chromosome,ClusterStart,ClusterEnd,ClusterID,AvgConversionPct,ConversionEventCountG,SdevConversionPct, MaxConversionPct ,Strand #out #Chromosome,ClusterStart,ClusterEnd,ClusterID_ClusterSequence_ReadCount_ModeLocation_ConversionLocationCount_ConversionEventCountC_NonConversionEventCount_ModeScore_AvgConversionPct_ConversionEventCountG_SdevConversionPct, MaxConversionPct ,Strand # bedtools intersect -a sh-clusters-0hrep1.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-0hrep1.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk > sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-2hrep1.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-2hrep1.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-6hrep1.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-6hrep1.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-0hrep2.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-0hrep2.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk > sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-2hrep2.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-2hrep2.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-6hrep2.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-6hrep2.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-0hrep3.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-0hrep3.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk > sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-2hrep3.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-2hrep3.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-6hrep3.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-6hrep3.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IFN.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-IFN.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IGG.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-IGG.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IL4.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-IL4.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 # separate plus strand results for i in sh-clusters-*1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 do wc $i awk -f ../filterPlusStrand.awk $i > $i.plus wc !$ done 754552 4527312 131501428 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 406385 2438310 71003130 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus 508797 3052782 88325829 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 275171 1651026 47880004 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus 372362 2234172 63783284 sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 200678 1204068 34448891 sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus 1118143 6708858 197457040 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2 607183 3643098 107466384 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus #remove IGG regions for i in sh-clusters-*1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus do wc $i bedtools intersect -a $i -b sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus -v -s |sort -k1,1 -k2,2n > $i.noIGG wc !$ done 406385 2438310 71003130 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus 372242 2233452 64914642 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG 275171 1651026 47880004 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus 249803 1498818 43382238 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG 200678 1204068 34448891 sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus 0 0 0 sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG 607183 3643098 107466384 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus 543841 3263046 95912512 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG #topuniform=max(which(lp8>0.05)); #highest modscore that is not uniformly distributed Rscript /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/get_modescore_hist_1kIntrons.r modscore_cutoff for IFN 0.917 0.551879409932128 modscore_cutoff for IL4 0.959 0.117435487674906 modscore_cutoff for 0h_rep1 0.959 0.0625273967265635 "modscore_cutoff for 0h_rep2 0.945 0.103475484554532" "modscore_cutoff for 0h_rep3 0.945 0.124099813055241" "modscore_cutoff for 2h_rep1 0.962 0.0898276601965392" "modscore_cutoff for 2h_rep2 0.957 0.250358822416992" "modscore_cutoff for 2h_rep3 0.953 0.0684610535576249" "modscore_cutoff for 6h_rep1 0.951 0.157704846747281" "modscore_cutoff for 6h_rep2 0.952 0.397195483078005" "modscore_cutoff for 6h_rep3 0.918 0.0556072580989269" awk -v th=0.917 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ # 31723 190338 5688399 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt awk -v th=0.959 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ # 48906 293436 8984444 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt awk -v th=0.959 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ awk -v th=0.945 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ awk -v th=0.945 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ awk -v th=0.962 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ awk -v th=0.957 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ awk -v th=0.953 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ awk -v th=0.951 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ awk -v th=0.952 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ awk -v th=0.918 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ #2do include introns+cds # filter protein_coding_genes and add annotation from /data/results/reference/mmu/mm9/1kIntrons-stranded/Mus_musculus.NCBIM37.64-toMM9.headers for i in *txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt do awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate-ExonIntron1.awk $i |sort -k1,1 -k4,4 -k2,2n -k5,5n > $i.anno1.csv done