cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b # step 1+2 of README-paralyze3.txt # paralyzer to bed, more than 5 TtoC for i in sh-clusters*txt2.csv do echo $i awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2bed-gt5tc.awk $i > $i.bed.gt5tc done # link files for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-distributions*.txt2.csv do ln -s $i done #get avg+max TtoC (note >100% bug in /data/images/proton/DKlab/mr/parclip/paralyzer/README.PARalyzer_v1_1_src.txt, clipped to 100%) for i in sh-distributions*.txt2.csv do cat $i| awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/get-TtoC-conversionPct2.awk > $i".avg.csv" done # to bed for i in sh-distributions*.txt2.csv.avg.csv do cat $i|awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa-dist2bed.awk > $i".bed" done # intersect maxTtoC_gt_0.25 with clusters #/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/ sh-distributions-0hrep1.txt2.csv.avg.csv.bed sh-distributions-0hrep2.txt2.csv.avg.csv.bed sh-distributions-0hrep3.txt2.csv.avg.csv.bed sh-distributions-2hrep1.txt2.csv.avg.csv.bed sh-distributions-2hrep2.txt2.csv.avg.csv.bed sh-distributions-2hrep3.txt2.csv.avg.csv.bed sh-distributions-6hrep1.txt2.csv.avg.csv.bed sh-distributions-6hrep2.txt2.csv.avg.csv.bed sh-distributions-6hrep3.txt2.csv.avg.csv.bed sh-distributions-IFN.txt2.csv.avg.csv.bed sh-distributions-IGG.txt2.csv.avg.csv.bed sh-distributions-IL4.txt2.csv.avg.csv.bed #with sh-clusters-0hrep1.txt2.csv.bed.gt5tc sh-clusters-0hrep2.txt2.csv.bed.gt5tc sh-clusters-0hrep3.txt2.csv.bed.gt5tc sh-clusters-2hrep1.txt2.csv.bed.gt5tc sh-clusters-2hrep2.txt2.csv.bed.gt5tc sh-clusters-2hrep3.txt2.csv.bed.gt5tc sh-clusters-6hrep1.txt2.csv.bed.gt5tc sh-clusters-6hrep2.txt2.csv.bed.gt5tc sh-clusters-6hrep3.txt2.csv.bed.gt5tc sh-clusters-IFN.txt2.csv.bed.gt5tc sh-clusters-IGG.txt2.csv.bed.gt5tc sh-clusters-IL4.txt2.csv.bed.gt5tc #is bedtools intersect -a sh-clusters-0hrep1.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-0hrep1.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk > sh-clusters-0hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-0hrep2.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-0hrep2.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-0hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-0hrep3.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-0hrep3.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-0hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-2hrep1.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-2hrep1.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-2hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-2hrep2.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-2hrep2.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-2hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-2hrep3.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-2hrep3.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-2hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-6hrep1.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-6hrep1.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-6hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-6hrep2.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-6hrep2.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-6hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-6hrep3.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-6hrep3.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-6hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IFN.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-IFN.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-IFN.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IGG.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-IGG.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IL4.txt2.csv.bed.gt5tc -b /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/sh-distributions-IL4.txt2.csv.avg.csv.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct1.awk> sh-clusters-IL4.txt2.csv.bed.gt5tc.gt0.25TtoC2 # wc *gt0.25TtoC2 # # strand stats for i in sh-clusters-*gt0.25TtoC2 do echo $i awk -f ../strandStats1.awk $i done sh-clusters-0hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 135421 plus_strand 73876 54.5528 % minus_strand 61545 45.4472 % sh-clusters-0hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 79000 plus_strand 44080 55.7975 % minus_strand 34920 44.2025 % sh-clusters-0hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 221471 plus_strand 122914 55.4989 % minus_strand 98557 44.5011 % sh-clusters-2hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 109197 plus_strand 61910 56.6957 % minus_strand 47287 43.3043 % sh-clusters-2hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 131255 plus_strand 73340 55.876 % minus_strand 57915 44.124 % sh-clusters-2hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 126346 plus_strand 68649 54.3341 % minus_strand 57697 45.6659 % sh-clusters-6hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 193097 plus_strand 110711 57.3344 % minus_strand 82386 42.6656 % sh-clusters-6hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 172278 plus_strand 96480 56.0025 % minus_strand 75798 43.9975 % sh-clusters-6hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 85479 plus_strand 49788 58.2459 % minus_strand 35691 41.7541 % sh-clusters-IFN.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 102563 plus_strand 57299 55.8671 % minus_strand 45264 44.1329 % sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 67597 plus_strand 37734 55.822 % minus_strand 29863 44.178 % sh-clusters-IL4.txt2.csv.bed.gt5tc.gt0.25TtoC nclusters 185857 plus_strand 103278 55.5685 % minus_strand 82579 44.4315 % # separate plus strand results for i in sh-c*gt0.25TtoC2 do wc $i awk -f ../filterPlusStrand.awk $i > $i.plus wc !$ done 135421 812526 19430092 sh-clusters-0hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2 73876 443256 10585573 sh-clusters-0hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 79000 474000 11189668 sh-clusters-0hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2 44080 264480 6249763 sh-clusters-0hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 221471 1328826 32059476 sh-clusters-0hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2 122914 737484 17807563 sh-clusters-0hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 109197 655182 15642473 sh-clusters-2hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2 61910 371460 8874897 sh-clusters-2hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 131255 787530 18975916 sh-clusters-2hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2 73340 440040 10612998 sh-clusters-2hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 126346 758076 18043607 sh-clusters-2hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2 68649 411894 9788330 sh-clusters-2hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 193097 1158582 27384250 sh-clusters-6hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2 110711 664266 15711925 sh-clusters-6hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 172278 1033668 24995989 sh-clusters-6hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2 96480 578880 13998043 sh-clusters-6hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 85479 512874 12162593 sh-clusters-6hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2 49788 298728 7095258 sh-clusters-6hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 102563 615378 14597768 sh-clusters-IFN.txt2.csv.bed.gt5tc.gt0.25TtoC2 57299 343794 8166438 sh-clusters-IFN.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 67597 405582 9428089 sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC2 37734 226404 5265322 sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus 185857 1115142 26837514 sh-clusters-IL4.txt2.csv.bed.gt5tc.gt0.25TtoC2 103278 619668 14897069 sh-clusters-IL4.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus #remove IGG regions for i in sh-clusters-*gt0.25TtoC2.plus do wc $i bedtools intersect -a $i -b sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus -v -s |sort -k1,1 -k2,2n > $i.noIGG wc !$ done 73876 443256 9095412 sh-clusters-0hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 68230 409380 8377155 sh-clusters-0hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 44080 264480 5362648 sh-clusters-0hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 40863 245178 4962377 sh-clusters-0hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 122914 737484 15311318 sh-clusters-0hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 117165 702990 14561671 sh-clusters-0hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 61910 371460 7625144 sh-clusters-2hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 55531 333186 6812745 sh-clusters-2hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 73340 440040 9130130 sh-clusters-2hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 68652 411912 8529155 sh-clusters-2hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 68649 411894 8404346 sh-clusters-2hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 64209 385254 7843126 sh-clusters-2hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 110711 664266 13468363 sh-clusters-6hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 103984 623904 12612750 sh-clusters-6hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 96480 578880 12044433 sh-clusters-6hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 90418 542508 11258588 sh-clusters-6hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 49788 298728 6092669 sh-clusters-6hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 46381 278286 5667245 sh-clusters-6hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 57299 343794 7010472 sh-clusters-IFN.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 52611 315666 6420070 sh-clusters-IFN.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 37734 226404 4507031 sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 0 0 0 sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG 103278 619668 12803866 sh-clusters-IL4.txt2.csv.bed.gt5tc.gt0.25TtoC.plus 94689 568134 11694649 sh-clusters-IL4.txt2.csv.bed.gt5tc.gt0.25TtoC.plus.noIGG #2 of 3 intersection bedtools multiinter -i sh-clusters-0hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG sh-clusters-0hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG sh-clusters-0hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc bedtools multiinter -i sh-clusters-2hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG sh-clusters-2hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG sh-clusters-2hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc bedtools multiinter -i sh-clusters-6hrep1.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG sh-clusters-6hrep2.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG sh-clusters-6hrep3.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-0h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc | bedtools merge -i - > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt2of3 wc !$ 17734 53202 504139 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt2of3 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-2h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc | bedtools merge -i - > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt2of3 wc !$ 15155 45465 430087 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt2of3 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-6h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc | bedtools merge -i - > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt2of3 wc !$ 24342 73026 690248 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt2of3 awk -v th=2 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-0h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc | bedtools merge -i - > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt3of3 wc !$ 918 2754 26121 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt3of3 awk -v th=2 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-2h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc | bedtools merge -i - > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt3of3 wc !$ 910 2730 25779 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt3of3 awk -v th=2 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-6h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc | bedtools merge -i - > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt3of3 wc !$ 1518 4554 43124 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.intersection-all.bed.gt5tc.gt3of3 mkdir /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc_gt0.25TtoC2 cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc_gt0.25TtoC2 for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/*gt0.25TtoC2*of3 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 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus |sort -k1,1 -k4,4 -k2,2n -k5,5n > sh-clusters-IGG.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.anno.csv awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-IFN.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG |sort -k1,1 -k4,4 -k2,2n -k5,5n > sh-clusters-IFN.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG.anno.csv awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-IL4.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG |sort -k1,1 -k4,4 -k2,2n -k5,5n > sh-clusters-IL4.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG.anno.csv # link source of merged files for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-?hrep?.txt2.csv.bed.gt5tc.gt0.25TtoC2.plus.noIGG do ln -s $i done