# gene lengths awk -f /data/results/tools/rnaseq/get-gene-length1.awk /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf > /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gene-lenghts.txt require(edgeR) gl=read.table("~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq/deg/Mus_musculus.NCBIM37.64-toMM9.gene-lenghts.txt",sep="\t") gl.names=gl$V1; #rnaseqMatrix1= read.table("gene_counts_merged_k20_NCBIM37.64.txt",header=T,sep="\t",skip=1) rnaseqMatrix1= read.table("~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq/stringtie2/gene_counts_merged_k20_NCBIM37.64_id.txt",header=T,sep="\t",skip=1) rnaseqMatrix0 =rnaseqMatrix1[,7:dim(rnaseqMatrix1)[2]]; rownames(rnaseqMatrix0)=rnaseqMatrix1$Geneid; #rnaseqMatrix = rnaseqMatrix0[rowSums(rnaseqMatrix0)>=2,] for (i in 1:dim(rnaseqMatrix0)[2]) { print (colnames(rnaseqMatrix0)[i]) print (summary(rnaseqMatrix0[,i]>0)) } for (i in 1:dim(rnaseqMatrix0)[2]) { print (colnames(rnaseqMatrix0)[i]) print (summary(rnaseqMatrix0[,i]>1)) } colnames(rnaseqMatrix0) [1] "wt01_trm_k20.bam" "wt02_trm_k20.bam" "wt21_trm_k20.bam" [4] "wt22_trm_k20.bam" "wt61_trm_k20.bam" "wt62_trm_k20.bam" [7] "wtIFN_1_trm_k20.bam" "wtIFN_2_trm_k20.bam" "wtIL4_1_trm_k20.bam" [10] "wtIL4_2_trm_k20.bam" "KO01_trm_k20.bam" "KO02_trm_k20.bam" [13] "KO21_trm_k20.bam" "KO22_trm_k20.bam" "KO61_trm_k20.bam" [16] "KO62_trm_k20.bam" "KOIFN_1_trm_k20.bam" "KOIFN_2_trm_k20.bam" [19] "KOIL4_1_trm_k20.bam" "KOIL4_2_trm_k20.bam" col_ordering = c(11,12,1,2)#0h rnaseqMatrix =rnaseqMatrix0[,col_ordering]; rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=2,] conditions = factor(c("KO","KO","WT","WT")); exp_study = DGEList(counts=rnaseqMatrix, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study) tTags = topTags(et,n=NULL,adjust.method = "fdr") #r <- rownames(topTags(et)$table) r <- rownames(tTags) c=cpm(exp_study)[r, order(exp_study$samples$group)] x=cbind(as.data.frame(tTags), gl[rownames(tTags),2],gl[rownames(tTags),3],c,0.001*gl[rownames(tTags),3]*c) x=cbind(x,0.5*(x[,10]+x[,11]),0.5*(x[,12]+x[,13])) y=x[ (x[,14]>1)&(x[,15]>1),] plot(log2(y[,14]),log2(y[,15]),pch=".") #x=cbind(as.data.frame(tTags),c) summary(de <- decideTestsDGE(et, p=0.05)) #detags <- rownames(exp_study)[as.logical(de)] #plotSmear(et, de.tags=detags) #abline(h = c(-1, 1), col = "blue") write.table(tTags, file="edgeRgenes-0h.csv") write.table(x, file="edgeRgenesExpr-0h.csv") #-1 101 #0 22027 #1 113 col_ordering = c(17,18,7,8)#IFN rnaseqMatrix =rnaseqMatrix0[,col_ordering]; rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=2,] exp_study = DGEList(counts=rnaseqMatrix, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study) tTags = topTags(et,n=NULL,adjust.method = "fdr") r <- rownames(tTags) c=cpm(exp_study)[r, order(exp_study$samples$group)] x=cbind(as.data.frame(tTags), gl[rownames(tTags),2],gl[rownames(tTags),3],c,0.001*gl[rownames(tTags),3]*c) x=cbind(x,0.5*(x[,10]+x[,11]),0.5*(x[,12]+x[,13])) y=x[ (x[,14]>1)&(x[,15]>1),] write.table(tTags, file="edgeRgenes-IFN.csv") write.table(x, file="edgeRgenesExpr-IFN.csv") summary(de <- decideTestsDGE(et, p=0.05)) #-1 73 #0 19924 #1 126 col_ordering = c(19,20,9,10)#IL4 rnaseqMatrix =rnaseqMatrix0[,col_ordering]; rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=2,] exp_study = DGEList(counts=rnaseqMatrix, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study) tTags = topTags(et,n=NULL,adjust.method = "fdr") r <- rownames(tTags) c=cpm(exp_study)[r, order(exp_study$samples$group)] x=cbind(as.data.frame(tTags), gl[rownames(tTags),2],gl[rownames(tTags),3],c,0.001*gl[rownames(tTags),3]*c) x=cbind(x,0.5*(x[,10]+x[,11]),0.5*(x[,12]+x[,13])) y=x[ (x[,14]>1)&(x[,15]>1),] write.table(tTags, file="edgeRgenes-IL4.csv") write.table(x, file="edgeRgenesExpr-IL4.csv") summary(de <- decideTestsDGE(et, p=0.05)) #-1 112 #0 21094 #1 77 #gn=rownames(tTags) [1] "wt01_trm_k20.bam" Mode FALSE TRUE NA's logical 12861 21092 0 [1] "wt02_trm_k20.bam" Mode FALSE TRUE NA's logical 13911 20042 0 [1] "wt21_trm_k20.bam" Mode FALSE TRUE NA's logical 14501 19452 0 [1] "wt22_trm_k20.bam" Mode FALSE TRUE NA's logical 14601 19352 0 [1] "wt61_trm_k20.bam" Mode FALSE TRUE NA's logical 13679 20274 0 [1] "wt62_trm_k20.bam" Mode FALSE TRUE NA's logical 14529 19424 0 [1] "wtIFN_1_trm_k20.bam" Mode FALSE TRUE NA's logical 15251 18702 0 [1] "wtIFN_2_trm_k20.bam" Mode FALSE TRUE NA's logical 14830 19123 0 [1] "wtIL4_1_trm_k20.bam" Mode FALSE TRUE NA's logical 13961 19992 0 [1] "wtIL4_2_trm_k20.bam" Mode FALSE TRUE NA's logical 14320 19633 0 [1] "KO01_trm_k20.bam" Mode FALSE TRUE NA's logical 13552 20401 0 [1] "KO02_trm_k20.bam" Mode FALSE TRUE NA's logical 12865 21088 0 [1] "KO21_trm_k20.bam" Mode FALSE TRUE NA's logical 13076 20877 0 [1] "KO22_trm_k20.bam" Mode FALSE TRUE NA's logical 12736 21217 0 [1] "KO61_trm_k20.bam" Mode FALSE TRUE NA's logical 13504 20449 0 [1] "KO62_trm_k20.bam" Mode FALSE TRUE NA's logical 13610 20343 0 [1] "KOIFN_1_trm_k20.bam" Mode FALSE TRUE NA's logical 14914 19039 0 [1] "KOIFN_2_trm_k20.bam" Mode FALSE TRUE NA's logical 15089 18864 0 [1] "KOIL4_1_trm_k20.bam" Mode FALSE TRUE NA's logical 13771 20182 0 [1] "KOIL4_2_trm_k20.bam" Mode FALSE TRUE NA's logical 13831 20122 0 # multimapped reads: for i in *trm_k20.bam > do > echo $i > samtools view -F 4 $i |awk -f /data/images/proton/DKlab/mr/rnaseq/get-multimap-stats-pe.awk > done KO01_trm_k20.bam #reads 46664885 #mappings 104515302 1 1045225 2.23985 2 42933201 92.0032 3 31783 0.068109 4 1752154 3.75476 5 6982 0.014962 6 351719 0.753712 7 3372 0.00722599 8 164740 0.353028 9 1048 0.0022458 10 70461 0.150994 11 936 0.00200579 12 108284 0.232046 13 557 0.00119362 14 26319 0.0564 15 369 0.000790744 16 17125 0.0366978 17 172 0.000368586 18 20896 0.0447789 19 162 0.000347156 20 24664 0.0528534 21 563 0.00120647 22 12534 0.0268596 23 26 5.57164e-05 24 6829 0.0146341 25 11 2.35723e-05 26 8070 0.0172935 27 5 1.07147e-05 28 7800 0.0167149 29 4 8.57176e-06 30 8597 0.0184228 31 6 1.28576e-05 32 4630 0.00992181 34 3984 0.00853747 36 5233 0.011214 37 3 6.42882e-06 38 4647 0.00995824 39 4 8.57176e-06 40 41770 0.0895106 #uniq. mapped reads 44223707 : (94.7687 pct) #multimapped reads 2441178 : (5.2313 pct) KO02_trm_k20.bam #reads 58569788 #mappings 131362490 1 1274216 2.17555 2 53930237 92.0786 3 30899 0.0527559 4 2190850 3.74058 5 6714 0.0114632 6 441460 0.753733 7 3255 0.00555747 8 190424 0.325123 9 1126 0.00192249 10 83476 0.142524 11 1052 0.00179615 12 172536 0.294582 13 518 0.000884415 14 30538 0.0521395 15 352 0.000600992 16 21478 0.0366708 17 176 0.000300496 18 28355 0.0484123 19 103 0.000175859 20 33454 0.0571182 21 489 0.000834901 22 15998 0.0273144 23 24 4.09768e-05 24 7514 0.0128291 25 28 4.78062e-05 26 10086 0.0172205 27 6 1.02442e-05 28 8600 0.0146833 29 9 1.53663e-05 30 11367 0.0194076 31 4 6.82946e-06 32 6011 0.010263 33 4 6.82946e-06 34 5372 0.00917196 36 6407 0.0109391 37 1 1.70736e-06 38 5751 0.00981906 40 50898 0.0869015 #uniq. mapped reads 55543037 : (94.8322 pct) #multimapped reads 3026751 : (5.16777 pct) KO21_trm_k20.bam #reads 56466268 #mappings 126992280 1 1201647 2.12808 2 51997651 92.0862 3 24870 0.044044 4 2090116 3.70153 5 4519 0.00800301 6 487489 0.863328 7 1742 0.00308503 8 184168 0.326156 9 978 0.00173201 10 76558 0.135582 11 910 0.00161158 12 157181 0.278363 13 473 0.000837668 14 27725 0.0491001 15 404 0.000715471 16 18641 0.0330126 17 211 0.000373674 18 27007 0.0478286 19 175 0.00030992 20 32559 0.057661 21 691 0.00122374 22 14427 0.0255498 23 47 8.32355e-05 24 7622 0.0134983 25 20 3.54194e-05 26 8693 0.015395 27 22 3.89613e-05 28 8170 0.0144688 29 10 1.77097e-05 30 10121 0.017924 31 10 1.77097e-05 32 5936 0.0105125 33 3 5.31291e-06 34 5460 0.00966949 35 5 8.85484e-06 36 6307 0.0111695 37 4 7.08388e-06 38 6564 0.0116246 39 1 1.77097e-06 40 57131 0.101177 #uniq. mapped reads 53508583 : (94.762 pct) #multimapped reads 2957685 : (5.23797 pct) KO22_trm_k20.bam #reads 55585677 #mappings 125267898 1 1209291 2.17554 2 51183804 92.0809 3 31612 0.0568708 4 2005730 3.60836 5 6587 0.0118502 6 474428 0.853508 7 3284 0.005908 8 182051 0.327514 9 1041 0.00187278 10 77719 0.139818 11 922 0.0016587 12 164449 0.295848 13 534 0.000960679 14 28129 0.0506048 15 402 0.000723208 16 18523 0.0333233 17 208 0.000374197 18 26821 0.0482516 19 215 0.00038679 20 34041 0.0612406 21 703 0.00126471 22 14393 0.0258934 23 35 6.29659e-05 24 8355 0.0150309 25 12 2.15883e-05 26 9507 0.0171033 27 23 4.13776e-05 28 8585 0.0154446 29 12 2.15883e-05 30 10235 0.018413 31 12 2.15883e-05 32 5955 0.0107132 33 5 8.99512e-06 34 5324 0.00957801 35 1 1.79902e-06 36 6670 0.0119995 37 1 1.79902e-06 38 6675 0.0120085 40 59383 0.106831 #uniq. mapped reads 52711017 : (94.8284 pct) #multimapped reads 2874660 : (5.17158 pct) KO61_trm_k20.bam #reads 52945443 #mappings 119746689 1 1256881 2.37392 2 48646203 91.8799 3 24898 0.0470258 4 1799137 3.3981 5 4814 0.00909238 6 566895 1.07072 7 2111 0.00398712 8 173833 0.328325 9 1129 0.00213238 10 74918 0.1415 11 962 0.00181696 12 144222 0.272397 13 505 0.000953812 14 26983 0.0509638 15 374 0.000706388 16 18023 0.0340407 17 184 0.000347528 18 25971 0.0490524 19 189 0.000356971 20 33409 0.0631008 21 686 0.00129567 22 16683 0.0315098 23 30 5.66621e-05 24 9228 0.0174293 25 26 4.91072e-05 26 10530 0.0198884 27 18 3.39973e-05 28 12122 0.0228953 29 9 1.69986e-05 30 10027 0.0189384 31 5 9.44368e-06 32 6326 0.0119481 33 2 3.77747e-06 34 5106 0.00964389 35 2 3.77747e-06 36 6822 0.012885 37 6 1.13324e-05 38 7042 0.0133005 39 4 7.55495e-06 40 59128 0.111677 #uniq. mapped reads 50195415 : (94.8059 pct) #multimapped reads 2750028 : (5.19408 pct) KO62_trm_k20.bam #reads 63351563 #mappings 142858436 1 1521659 2.40193 2 58160983 91.8067 3 31640 0.0499435 4 2212966 3.49315 5 6484 0.0102349 6 669880 1.0574 7 2780 0.00438821 8 209330 0.330426 9 1480 0.00233617 10 91824 0.144944 11 1066 0.00168267 12 155593 0.245602 13 666 0.00105128 14 33661 0.0531337 15 418 0.00065981 16 23051 0.0363858 17 255 0.000402516 18 29047 0.0458505 19 254 0.000400937 20 35922 0.0567026 21 853 0.00134645 22 17431 0.0275147 23 45 7.10322e-05 24 12141 0.0191645 25 18 2.84129e-05 26 11499 0.0181511 27 14 2.20989e-05 28 13182 0.0208077 29 13 2.05204e-05 30 11337 0.0178954 31 13 2.05204e-05 32 7283 0.0114962 33 7 1.10495e-05 34 5629 0.00888534 35 3 4.73548e-06 36 7719 0.0121844 37 1 1.57849e-06 38 8280 0.0130699 39 1 1.57849e-06 40 67135 0.105972 #uniq. mapped reads 60018477 : (94.7387 pct) #multimapped reads 3333086 : (5.26125 pct) KOIFN_1_trm_k20.bam #reads 58331960 #mappings 131767702 1 1535845 2.63294 2 53367686 91.4896 3 26213 0.0449376 4 2071118 3.55057 5 5426 0.00930193 6 647014 1.10919 7 2474 0.00424124 8 171342 0.293736 9 1560 0.00267435 10 81137 0.139095 11 1117 0.0019149 12 143342 0.245735 13 718 0.00123089 14 33182 0.0568848 15 477 0.000817734 16 21739 0.0372677 17 202 0.000346294 18 27326 0.0468457 19 286 0.000490297 20 33514 0.0574539 21 813 0.00139375 22 18349 0.0314562 23 44 7.54303e-05 24 13094 0.0224474 25 9 1.54289e-05 26 12064 0.0206816 27 5 8.57163e-06 28 13190 0.022612 29 5 8.57163e-06 30 10347 0.0177381 31 5 8.57163e-06 32 7381 0.0126534 33 3 5.14298e-06 34 5707 0.00978366 35 3 5.14298e-06 36 8075 0.0138432 37 3 5.14298e-06 38 9345 0.0160204 40 61800 0.105945 #uniq. mapped reads 55213057 : (94.6532 pct) #multimapped reads 3118903 : (5.34682 pct) KOIFN_2_trm_k20.bam #reads 50652530 #mappings 114760481 1 1282036 2.53104 2 46374468 91.5541 3 23147 0.0456976 4 1757864 3.47044 5 4147 0.00818715 6 593981 1.17266 7 1803 0.00355955 8 163425 0.322639 9 1362 0.00268891 10 71211 0.140587 11 889 0.00175509 12 137166 0.270798 13 577 0.00113913 14 26355 0.052031 15 330 0.000651498 16 20236 0.0399506 17 195 0.000384976 18 24657 0.0486787 19 270 0.000533043 20 30584 0.06038 21 665 0.00131287 22 14413 0.0284546 23 45 8.88406e-05 24 11504 0.0227116 25 8 1.57939e-05 26 9856 0.0194581 27 4 7.89694e-06 28 10922 0.0215626 29 15 2.96135e-05 30 8843 0.0174582 31 5 9.87118e-06 32 6309 0.0124554 33 1 1.97424e-06 34 4836 0.0095474 36 6855 0.0135334 37 2 3.94847e-06 38 8357 0.0164987 39 4 7.89694e-06 40 55183 0.108944 #uniq. mapped reads 47938390 : (94.6416 pct) #multimapped reads 2714140 : (5.35835 pct) KOIL4_1_trm_k20.bam #reads 58368276 #mappings 130428635 1 1671041 2.86293 2 53163396 91.0827 3 28741 0.0492408 4 2428501 4.16065 5 6599 0.0113058 6 443524 0.759872 7 2863 0.00490506 8 173071 0.296516 9 1422 0.00243625 10 86180 0.147649 11 1351 0.00231461 12 114682 0.19648 13 891 0.00152651 14 36040 0.0617459 15 486 0.000832644 16 23765 0.0407156 17 241 0.000412896 18 24567 0.0420896 19 237 0.000406042 20 30167 0.0516839 21 750 0.00128494 22 16487 0.0282465 23 41 7.02436e-05 24 9018 0.0154502 25 19 3.25519e-05 26 9994 0.0171223 27 3 5.13978e-06 28 8275 0.0141772 29 8 1.37061e-05 30 9624 0.0164884 31 6 1.02796e-05 32 5761 0.00987009 33 4 6.85304e-06 34 5199 0.00890724 35 2 3.42652e-06 36 6476 0.0110951 37 2 3.42652e-06 38 8460 0.0144942 39 2 3.42652e-06 40 50380 0.086314 #uniq. mapped reads 55122877 : (94.4398 pct) #multimapped reads 3245399 : (5.56021 pct) KOIL4_2_trm_k20.bam #reads 60083101 #mappings 133866223 1 1843453 3.06817 2 54608430 90.8882 3 36195 0.0602416 4 2435360 4.05332 5 7883 0.0131202 6 495442 0.824595 7 3500 0.00582527 8 204895 0.341019 9 1461 0.00243163 10 85894 0.142959 11 1394 0.00232012 12 124814 0.207736 13 974 0.00162109 14 34301 0.0570893 15 513 0.000853817 16 22506 0.0374581 17 247 0.000411097 18 23754 0.0395352 19 235 0.000391125 20 29016 0.0482931 21 785 0.00130652 22 16009 0.0266448 23 48 7.98894e-05 24 8536 0.014207 25 18 2.99585e-05 26 9982 0.0166137 27 9 1.49793e-05 28 9040 0.0150458 29 8 1.33149e-05 30 8923 0.0148511 31 7 1.16505e-05 32 5800 0.0096533 33 3 4.99308e-06 34 5042 0.00839171 35 2 3.32872e-06 36 6165 0.0102608 37 1 1.66436e-06 38 7901 0.0131501 39 3 4.99308e-06 40 44552 0.0741506 #uniq. mapped reads 56746515 : (94.4467 pct) #multimapped reads 3336586 : (5.55329 pct) wt01_trm_k20.bam #reads 41725733 #mappings 93530973 1 849607 2.03617 2 38511128 92.2959 3 20857 0.0499859 4 1593121 3.81808 5 4550 0.0109045 6 279820 0.670617 7 2448 0.00586688 8 115073 0.275784 9 646 0.00154821 10 58187 0.139451 11 707 0.0016944 12 106869 0.256123 13 405 0.000970624 14 21825 0.0523059 15 262 0.00062791 16 15563 0.0372983 17 120 0.000287592 18 20788 0.0498206 19 152 0.000364284 20 24163 0.0579091 21 392 0.000939468 22 12468 0.0298808 23 16 3.83456e-05 24 5691 0.0136391 25 13 3.11558e-05 26 8122 0.0194652 27 8 1.91728e-05 28 7212 0.0172843 29 4 9.58641e-06 30 7805 0.0187055 31 4 9.58641e-06 32 4953 0.0118704 33 1 2.3966e-06 34 4161 0.00997226 35 2 4.79321e-06 36 5381 0.0128961 38 4508 0.0108039 39 1 2.3966e-06 40 38700 0.0927485 #uniq. mapped reads 39585613 : (94.871 pct) #multimapped reads 2140120 : (5.12902 pct) wt02_trm_k20.bam #reads 42547634 #mappings 95427536 1 889475 2.09054 2 39232366 92.2081 3 29627 0.0696325 4 1595231 3.74928 5 7359 0.0172959 6 294646 0.692509 7 4135 0.00971852 8 127148 0.298837 9 715 0.00168047 10 65147 0.153115 11 808 0.00189905 12 118495 0.2785 13 430 0.00101063 14 23086 0.0542592 15 290 0.000681589 16 15029 0.0353228 17 135 0.000317291 18 20477 0.0481272 19 154 0.000361947 20 24769 0.0582148 21 345 0.000810856 22 12994 0.0305399 23 14 3.29043e-05 24 5439 0.0127833 25 19 4.46558e-05 26 8547 0.0200881 27 3 7.05092e-06 28 7460 0.0175333 29 6 1.41018e-05 30 7827 0.0183959 31 5 1.17515e-05 32 4402 0.0103461 33 3 7.05092e-06 34 4023 0.00945528 35 1 2.35031e-06 36 4897 0.0115095 38 4362 0.010252 40 37765 0.0887593 #uniq. mapped reads 40365892 : (94.8722 pct) #multimapped reads 2181742 : (5.12776 pct) wt21_trm_k20.bam #reads 39385612 #mappings 88386936 1 803802 2.04085 2 36372987 92.351 3 17379 0.0441253 4 1419788 3.60484 5 3644 0.00925211 6 316234 0.802918 7 1666 0.00422997 8 114843 0.291586 9 563 0.00142946 10 56239 0.142791 11 643 0.00163258 12 112619 0.285939 13 367 0.000931812 14 20134 0.0511202 15 275 0.000698225 16 13494 0.0342612 17 113 0.000286907 18 17757 0.045085 19 98 0.000248822 20 21976 0.055797 21 383 0.000972436 22 9772 0.0248111 23 14 3.5546e-05 24 5611 0.0142463 25 23 5.8397e-05 26 6175 0.0156783 27 3 7.61699e-06 28 5317 0.0134999 29 6 1.5234e-05 30 7193 0.018263 31 4 1.0156e-05 32 3846 0.00976499 33 1 2.539e-06 34 3615 0.00917848 36 4454 0.0113087 37 1 2.539e-06 38 4610 0.0117048 39 1 2.539e-06 40 39962 0.101463 #uniq. mapped reads 37398528 : (94.9548 pct) #multimapped reads 1987084 : (5.0452 pct) wt22_trm_k20.bam #reads 46338223 #mappings 104458556 1 950348 2.05089 2 42696316 92.1406 3 19774 0.0426732 4 1700808 3.67042 5 4103 0.00885446 6 406651 0.877571 7 1912 0.00412618 8 150793 0.325418 9 846 0.00182571 10 70361 0.151842 11 836 0.00180413 12 131189 0.283112 13 551 0.00118908 14 26197 0.0565343 15 359 0.000774738 16 17031 0.0367537 17 185 0.000399238 18 22015 0.0475094 19 200 0.000431609 20 27090 0.0584615 21 568 0.00122577 22 12578 0.0271439 23 35 7.55316e-05 24 8358 0.0180369 25 10 2.15805e-05 26 7769 0.0167659 27 10 2.15805e-05 28 7188 0.015512 29 9 1.94224e-05 30 8535 0.0184189 31 7 1.51063e-05 32 4532 0.00978026 33 2 4.31609e-06 34 4199 0.00906163 35 2 4.31609e-06 36 5038 0.0108722 37 3 6.47414e-06 38 5492 0.011852 40 46323 0.0999671 #uniq. mapped reads 43915588 : (94.7718 pct) #multimapped reads 2422635 : (5.22816 pct) wt61_trm_k20.bam #reads 45396485 #mappings 102615096 1 1134817 2.49979 2 41687668 91.8302 3 29013 0.0639102 4 1478726 3.25736 5 6208 0.0136751 6 494941 1.09026 7 3096 0.00681991 8 148321 0.326724 9 1102 0.0024275 10 65438 0.144148 11 687 0.00151333 12 131628 0.289952 13 450 0.000991266 14 24001 0.0528697 15 259 0.000570529 16 16301 0.0359081 17 151 0.000332625 18 23565 0.0519093 19 159 0.000350247 20 30167 0.0664523 21 582 0.00128204 22 13721 0.0302248 23 32 7.049e-05 24 7886 0.0173714 25 16 3.5245e-05 26 7668 0.0168912 27 8 1.76225e-05 28 8839 0.0194707 29 6 1.32169e-05 30 8704 0.0191733 31 4 8.81125e-06 32 5291 0.0116551 33 3 6.60844e-06 34 4176 0.00919895 35 1 2.20281e-06 36 5694 0.0125428 37 5 1.10141e-05 38 6298 0.0138733 39 1 2.20281e-06 40 50852 0.112017 #uniq. mapped reads 43085124 : (94.9085 pct) #multimapped reads 2311361 : (5.0915 pct) wt62_trm_k20.bam #reads 44000549 #mappings 99255530 1 971178 2.2072 2 40500884 92.0463 3 16833 0.0382563 4 1526329 3.46889 5 3505 0.00796581 6 475090 1.07974 7 1540 0.00349996 8 131291 0.298385 9 885 0.00201134 10 61231 0.13916 11 676 0.00153634 12 113958 0.258992 13 406 0.000922716 14 22474 0.0510766 15 268 0.000609083 16 15933 0.0362109 17 162 0.000368177 18 19617 0.0445835 19 167 0.000379541 20 25874 0.0588038 21 560 0.00127271 22 12530 0.0284769 23 35 7.95445e-05 24 7866 0.017877 25 16 3.63632e-05 26 7803 0.0177339 27 3 6.8181e-06 28 8300 0.0188634 29 3 6.8181e-06 30 7571 0.0172066 31 3 6.8181e-06 32 4969 0.011293 33 2 4.5454e-06 34 4005 0.00910216 35 2 4.5454e-06 36 5074 0.0115317 37 1 2.2727e-06 38 5639 0.0128157 39 1 2.2727e-06 40 47865 0.108783 #uniq. mapped reads 41706954 : (94.7873 pct) #multimapped reads 2293595 : (5.21265 pct) wtIFN_1_trm_k20.bam #reads 45489792 #mappings 102820055 1 1288311 2.83209 2 41523142 91.2801 3 24703 0.0543045 4 1565879 3.44226 5 4462 0.00980879 6 528100 1.16092 7 1952 0.00429107 8 151594 0.333248 9 1271 0.00279403 10 64411 0.141594 11 829 0.00182239 12 121695 0.267522 13 526 0.0011563 14 23569 0.0518116 15 382 0.000839749 16 16679 0.0366654 17 195 0.000428668 18 23007 0.0505762 19 218 0.000479228 20 28256 0.062115 21 635 0.00139592 22 13449 0.0295649 23 41 9.01301e-05 24 8760 0.0192571 25 10 2.1983e-05 26 8024 0.0176391 27 11 2.41812e-05 28 10114 0.0222336 29 3 6.59489e-06 30 7911 0.0173907 31 3 6.59489e-06 32 5418 0.0119104 33 2 4.39659e-06 34 4245 0.00933176 35 1 2.1983e-06 36 5914 0.0130007 37 4 8.79318e-06 38 7183 0.0157904 39 2 4.39659e-06 40 48881 0.107455 #uniq. mapped reads 43062964 : (94.6651 pct) #multimapped reads 2426828 : (5.33488 pct) wtIFN_2_trm_k20.bam #reads 60154107 #mappings 136652505 1 1513725 2.51641 2 54994070 91.422 3 29155 0.0484672 4 2127194 3.53624 5 5905 0.00981645 6 722759 1.20151 7 2767 0.00459985 8 216163 0.359349 9 1654 0.0027496 10 89898 0.149446 11 1079 0.00179373 12 159354 0.26491 13 737 0.00122519 14 33101 0.055027 15 470 0.000781327 16 23066 0.0383448 17 250 0.000415599 18 29827 0.0495843 19 288 0.00047877 20 38631 0.0642201 21 857 0.00142467 22 18009 0.0299381 23 40 6.64959e-05 24 12174 0.020238 25 16 2.65984e-05 26 11771 0.0195681 27 9 1.49616e-05 28 14278 0.0237357 29 12 1.99488e-05 30 10782 0.017924 31 6 9.97438e-06 32 7592 0.0126209 33 3 4.98719e-06 34 5810 0.00965853 35 2 3.32479e-06 36 7944 0.0132061 37 4 6.64959e-06 38 9703 0.0161302 39 2 3.32479e-06 40 65000 0.108056 #uniq. mapped reads 56845865 : (94.5004 pct) #multimapped reads 3308242 : (5.49961 pct) wtIL4_1_trm_k20.bam #reads 53622988 #mappings 120186902 1 1566220 2.9208 2 48701793 90.8226 3 34429 0.0642057 4 2241342 4.17982 5 6784 0.0126513 6 442154 0.824561 7 3315 0.00618205 8 207360 0.3867 9 1223 0.00228074 10 81214 0.151454 11 1164 0.00217071 12 118674 0.221312 13 856 0.00159633 14 30201 0.056321 15 430 0.000801895 16 19518 0.0363986 17 222 0.000414002 18 22756 0.042437 19 172 0.000320758 20 28137 0.0524719 21 577 0.00107603 22 14282 0.0266341 23 41 7.64597e-05 24 7533 0.0140481 25 20 3.72974e-05 26 9249 0.0172482 27 6 1.11892e-05 28 8206 0.0153031 29 3 5.59462e-06 30 9227 0.0172072 31 7 1.30541e-05 32 4950 0.00923112 33 2 3.72974e-06 34 4567 0.00851687 35 4 7.45949e-06 36 5531 0.0103146 37 1 1.86487e-06 38 7214 0.0134532 40 43604 0.0813159 #uniq. mapped reads 50543220 : (94.2566 pct) #multimapped reads 3079768 : (5.74337 pct) wtIL4_2_trm_k20.bam #reads 41102274 #mappings 92024031 1 1177368 2.86448 2 37416060 91.0316 3 22909 0.0557366 4 1653983 4.02407 5 4476 0.0108899 6 349127 0.84941 7 1970 0.00479292 8 159811 0.388813 9 1045 0.00254244 10 60095 0.146208 11 881 0.00214343 12 88229 0.214657 13 621 0.00151087 14 23517 0.0572158 15 311 0.000756649 16 16007 0.0389443 17 179 0.000435499 18 17041 0.04146 19 146 0.000355211 20 20101 0.0489048 21 514 0.00125054 22 10480 0.0254974 23 40 9.73182e-05 24 5786 0.0140771 25 13 3.16284e-05 26 6796 0.0165344 27 8 1.94636e-05 28 5863 0.0142644 29 8 1.94636e-05 30 6680 0.0162521 31 6 1.45977e-05 32 3911 0.00951529 33 5 1.21648e-05 34 3592 0.00873918 36 4487 0.0109167 38 5823 0.0141671 39 1 2.43296e-06 40 34384 0.0836547 #uniq. mapped reads 38800455 : (94.3998 pct) #multimapped reads 2301819 : (5.60022 pct) ]0;~/bak/doc/fleming/kafasla/DKlab/mr/rnaseqreczko@max:~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq$