diff --git a/RNA-seq/18-HEPG2_S18_L001_R1_001.fastq.gz b/RNA-seq/18-HEPG2_S18_L001_R1_001.fastq.gz new file mode 100644 index 0000000000000000000000000000000000000000..3ea2ad5b3718e6bab0b2166cc80dcc8454730024 --- /dev/null +++ b/RNA-seq/18-HEPG2_S18_L001_R1_001.fastq.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f253b34002205bcc134bf2655435210a6bed2fda1babcd07d861d9927ecec8a4 +size 775234329 diff --git a/RNA-seq/25-HCT116_S25_L002_R1_001.fastq.gz b/RNA-seq/25-HCT116_S25_L002_R1_001.fastq.gz new file mode 100644 index 0000000000000000000000000000000000000000..f942c0b9b727dc490675bd0b1637aff5a5f4575d --- /dev/null +++ b/RNA-seq/25-HCT116_S25_L002_R1_001.fastq.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8e2d1ecc75a51360722ac2fdd627e508f560ab6b878e3ae4de64c48bb507b104 +size 220362608 diff --git a/smRNA-seq/.ipynb_checkpoints/miRNA_analysis-checkpoint.ipynb b/smRNA-seq/.ipynb_checkpoints/miRNA_analysis-checkpoint.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..9e60cbbd55990c547d0733cd2b15e91efb2eab9e --- /dev/null +++ b/smRNA-seq/.ipynb_checkpoints/miRNA_analysis-checkpoint.ipynb @@ -0,0 +1,34 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 0 +} diff --git a/smRNA-seq/.ipynb_checkpoints/smRNA_process-checkpoint.ipynb b/smRNA-seq/.ipynb_checkpoints/smRNA_process-checkpoint.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..a31ec64765e786e66deeb3da41f505f7c8735fad --- /dev/null +++ b/smRNA-seq/.ipynb_checkpoints/smRNA_process-checkpoint.ipynb @@ -0,0 +1,426 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd" + ] + }, + { + "cell_type": "code", + "execution_count": 55, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "#append UMIs\n", + "nohup sh -c \"ls *_R1_001.fastq.gz | parallel -j12 -k python append_umi.py {}\" &" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "shopt -s extglob\n", + "for f in *.fastq.gz; do\n", + "out=${f/.fastq.gz/.trim.fastq.gz}\n", + "echo \"cutadapt -j 12 -m 15 -u 3 -a AAAAAAAAAAAAAAAA -o $out $f;\"\n", + "cutadapt -j 12 -m 15 -u 3 -a AAAAAAAAAAAAAAAA -o $out $f;\n", + "done" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "for f in *.trim.fastq.gz; do\n", + "out=${f/.trim.fastq.gz/.bam}\n", + "echo \"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x /avicenna/genomes/hg38/hg38 -U $f | samtools view - -Sb -h -t /avicenna/genomes/hg38/hg38.fa.fai -o $out\";\n", + "bowtie2 --sensitive --end-to-end -N 1 -p 12 -x /avicenna/genomes/hg38/hg38 -U $f | samtools view - -Sb -h -t /avicenna/genomes/hg38/hg38.fa.fai -o $out ;\n", + "done" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "for f in *.bam; do\n", + "out=${f/.bam/.srt.bam};\n", + "echo \"samtools sort -o $out $f\";\n", + "samtools sort -@ 12 -m 2G -o $out $f\n", + "samtools index $out;\n", + "done" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "for f in *.srt.bam; do\n", + "out=${f/.srt.bam/.srt.dd.bam};\n", + "echo \"umi_tools dedup -I $f -S $out\";\n", + "umi_tools dedup -I $f -S $out &\n", + "done" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "for f in *.srt.dd.bam; do\n", + "samtools index $f &\n", + "done" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "for f in *.dd.bam; do\n", + "out=${f/.dd.bam/.dd.bed}\n", + "bamToBed -i $f > $out\n", + "done" + ] + }, + { + "cell_type": "code", + "execution_count": 62, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "cat *.dd.bed | sort -k1,1 -k2,2n | \\\n", + "mergeBed -s -c 4,6 -o count,distinct -i stdin | \\\n", + "awk '{print $1 \"\\t\" $2 \"\\t\" $3 \"\\t\" $1\":\"$2\"-\"$3\":\"$5 \"\\t\" $4 \"\\t\" $5}' > combined_smRNA_loci.bed" + ] + }, + { + "cell_type": "code", + "execution_count": 63, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "#remove peaks with only one read\n", + "awk '{if($5>1) print}' combined_smRNA_loci.bed > combined_smRNA_loci.c.bed" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "for f in *.dd.bam; do\n", + "out=${f/.dd.bam/.tRNA.cnt}\n", + "echo \"samtools view -h $f | bamToBed -i stdin | intersectBed -s -wo -a stdin -b /avicenna/genomes/hg38/hg38_tRNA.bed | cut -f10 | sort | uniq -c | awk '{ print $2 \\\"\\t\\\" $1}' > $out\"\n", + "samtools view -h $f | bamToBed -i stdin | intersectBed -s -wo -a stdin -b /avicenna/genomes/hg38/hg38_tRNA.bed | cut -f10 | sort | uniq -c | awk '{ print $2 \"\\t\" $1}' > $out &\n", + "done" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash\n", + "for f in *.dd.bam; do\n", + "out=${f/.dd.bam/.smRNA.cnt}\n", + "echo \"samtools view -h $f | bamToBed -i stdin | intersectBed -s -wo -a stdin -b combined_smRNA_loci.c.bed | cut -f10 | sort | uniq -c | awk '{ print $2 \\\"\\t\\\" $1}' > $out\"\n", + "samtools view -h $f | bamToBed -i stdin | intersectBed -s -wo -a stdin -b combined_smRNA_loci.c.bed | cut -f10 | sort | uniq -c | awk '{ print $2 \"\\t\" $1}' > $out &\n", + "done" + ] + }, + { + "cell_type": "code", + "execution_count": 73, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The rpy2.ipython extension is already loaded. To reload it, use:\n", + " %reload_ext rpy2.ipython\n" + ] + } + ], + "source": [ + "import rpy2.ipython\n", + "%load_ext rpy2.ipython\n", + "import warnings\n", + "from rpy2.rinterface import RRuntimeWarning\n", + "warnings.filterwarnings(\"ignore\", category=RRuntimeWarning)" + ] + }, + { + "cell_type": "code", + "execution_count": 74, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + " A2508 A375 A549 BxPC3 C42Bu Colo320 H1299 H23u H358u\n", + "nm-tRNA-SerTGA-AGA-chr11-7 3 1 1 1 0 0 0 0 1\n", + "nm-tRNA-Tyr-ATA-chr11-8 1 0 0 0 1 0 0 0 0\n", + "nm-tRNA-Tyr-GTA-chr1-142 875 794 461 506 188 507 292 522 539\n", + "nm-tRNA-Tyr-GTA-chr14-8 867 766 407 462 192 528 281 504 557\n", + "nm-tRNA-Tyr-GTA-chr2-12 1 0 0 0 1 3 0 0 2\n", + "nm-tRNA-Tyr-GTA-chr21-2 866 767 441 469 169 503 292 573 574\n", + " HCC44 HCT116 HEK293T.1 HEK293T.16 HEK293T.26\n", + "nm-tRNA-SerTGA-AGA-chr11-7 0 0 2 1 2\n", + "nm-tRNA-Tyr-ATA-chr11-8 0 0 1 1 0\n", + "nm-tRNA-Tyr-GTA-chr1-142 508 470 308 338 519\n", + "nm-tRNA-Tyr-GTA-chr14-8 489 453 344 355 454\n", + "nm-tRNA-Tyr-GTA-chr2-12 0 0 1 1 0\n", + "nm-tRNA-Tyr-GTA-chr21-2 527 502 340 362 502\n", + " HEK293T.9 HEPG2 HS707A K562 LNCaP LS174T MCF7 MDA231\n", + "nm-tRNA-SerTGA-AGA-chr11-7 1 3 0 3 1 3 4 1\n", + "nm-tRNA-Tyr-ATA-chr11-8 0 0 0 1 2 0 0 0\n", + "nm-tRNA-Tyr-GTA-chr1-142 423 400 387 684 337 404 832 377\n", + "nm-tRNA-Tyr-GTA-chr14-8 438 358 384 730 322 405 863 373\n", + "nm-tRNA-Tyr-GTA-chr2-12 0 1 0 0 1 0 0 0\n", + "nm-tRNA-Tyr-GTA-chr21-2 439 395 339 716 293 349 868 393\n", + " MDA453 PACA2 PANC1 PC3 SW480u SW620u ZR751\n", + "nm-tRNA-SerTGA-AGA-chr11-7 6 0 1 0 1 1 0\n", + "nm-tRNA-Tyr-ATA-chr11-8 0 0 0 0 0 0 0\n", + "nm-tRNA-Tyr-GTA-chr1-142 458 529 239 295 447 613 315\n", + "nm-tRNA-Tyr-GTA-chr14-8 483 564 242 337 457 655 319\n", + "nm-tRNA-Tyr-GTA-chr2-12 0 0 0 0 1 0 0\n", + "nm-tRNA-Tyr-GTA-chr21-2 466 536 236 305 466 635 335\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "%%R\n", + "files<-list.files(pattern=\".tRNA.cnt\")\n", + "datalist = lapply(files, function(x){read.table(file=x,header=FALSE,col.names=c(\"tRF\", sub(\".srt.tRNA.cnt\", \"\", x)))})\n", + "m <- Reduce(function(...) merge(..., by=1, all = TRUE), datalist)\n", + "rownames(m) <- m[,1]\n", + "m[is.na(m)] <- 0\n", + "m <- m[,-1]\n", + "head(m)" + ] + }, + { + "cell_type": "code", + "execution_count": 75, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + " A2508 A375 A549 BxPC3 C42Bu Colo320 H1299\n", + "chr1_KI270706v1_random:16702-16720:+ 1 4 2 0 4 6 5\n", + " H23u H358u HCC44 HCT116 HEK293T.1\n", + "chr1_KI270706v1_random:16702-16720:+ 5 3 5 0 3\n", + " HEK293T.16 HEK293T.26 HEK293T.9 HEPG2\n", + "chr1_KI270706v1_random:16702-16720:+ 4 0 2 4\n", + " HS707A K562 LNCaP LS174T MCF7 MDA231\n", + "chr1_KI270706v1_random:16702-16720:+ 1 3 6 0 1 2\n", + " MDA453 PACA2 PANC1 PC3 SW480u SW620u ZR751\n", + "chr1_KI270706v1_random:16702-16720:+ 3 0 2 3 4 4 5\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "%%R\n", + "files<-list.files(pattern=\".smRNA.cnt\")\n", + "datalist = lapply(files, function(x){read.table(file=x,header=FALSE,col.names=c(\"smRNA\", sub(\".srt.smRNA.cnt\", \"\", x)))})\n", + "tmp <- Reduce(function(...) merge(..., by=1, all = TRUE), datalist)\n", + "rownames(tmp) <- tmp[,1]\n", + "tmp[is.na(tmp)] <- 0\n", + "tmp <- tmp[,-1]\n", + "head(tmp, n=1)" + ] + }, + { + "cell_type": "code", + "execution_count": 76, + "metadata": {}, + "outputs": [], + "source": [ + "%%R\n", + "library(DESeq2)\n", + "colData <- data.frame(cond=colnames(tmp), row.names=colnames(tmp))\n", + "dds <- DESeqDataSetFromMatrix(countData = tmp, colData=colData, design = ~ cond)" + ] + }, + { + "cell_type": "code", + "execution_count": 77, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + " A2508 A375 A549 BxPC3 C42Bu Colo320 H1299 \n", + " 0.8256935 0.9923271 1.1037352 1.0105470 1.0176283 1.4778089 0.9678724 \n", + " H23u H358u HCC44 HCT116 HEK293T.1 HEK293T.16 HEK293T.26 \n", + " 1.0353598 0.9567173 1.4534567 0.9563961 0.8791460 0.9661940 1.1574294 \n", + " HEK293T.9 HEPG2 HS707A K562 LNCaP LS174T MCF7 \n", + " 1.1136977 1.0220953 0.9445823 1.2421130 1.2262184 0.8602644 1.0403348 \n", + " MDA231 MDA453 PACA2 PANC1 PC3 SW480u SW620u \n", + " 1.1131138 1.0942638 1.1119712 0.7794847 0.7744898 1.1932962 1.0305997 \n", + " ZR751 \n", + " 0.8341806 \n" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "%%R\n", + "dds <- estimateSizeFactors(dds)\n", + "sf <- sizeFactors(dds)\n", + "ncu <- counts(dds, normalized=TRUE)\n", + "write.table(tmp, file=\"smRNA_counts.txt\", sep=\"\\t\", quote=FALSE, col.names=NA )\n", + "write.table(ncu, file=\"smRNA_norm-counts.txt\", sep=\"\\t\", quote=FALSE, col.names=NA )\n", + "sf" + ] + }, + { + "cell_type": "code", + "execution_count": 78, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + " A2508 A375 A549 BxPC3\n", + "nm-tRNA-SerTGA-AGA-chr11-7 3.633309 1.007732 0.9060144 0.9895631\n", + "nm-tRNA-Tyr-ATA-chr11-8 1.211103 0.000000 0.0000000 0.0000000\n", + "nm-tRNA-Tyr-GTA-chr1-142 1059.715236 800.139362 417.6726390 500.7189382\n", + "nm-tRNA-Tyr-GTA-chr14-8 1050.026411 771.922860 368.7478614 457.1781610\n", + "nm-tRNA-Tyr-GTA-chr2-12 1.211103 0.000000 0.0000000 0.0000000\n", + "nm-tRNA-Tyr-GTA-chr21-2 1048.815308 772.930593 399.5523510 464.1051028\n", + " C42Bu Colo320 H1299 H23u H358u\n", + "nm-tRNA-SerTGA-AGA-chr11-7 0.000000 0.000000 0.0000 0.0000 1.045241\n", + "nm-tRNA-Tyr-ATA-chr11-8 0.982677 0.000000 0.0000 0.0000 0.000000\n", + "nm-tRNA-Tyr-GTA-chr1-142 184.743282 343.075491 301.6927 504.1726 563.384822\n", + "nm-tRNA-Tyr-GTA-chr14-8 188.673990 357.285718 290.3275 486.7873 582.199158\n", + "nm-tRNA-Tyr-GTA-chr2-12 0.982677 2.030032 0.0000 0.0000 2.090482\n", + "nm-tRNA-Tyr-GTA-chr21-2 166.072418 340.368781 301.6927 553.4308 599.968253\n", + " HCC44 HCT116 HEK293T.1 HEK293T.16 HEK293T.26\n", + "nm-tRNA-SerTGA-AGA-chr11-7 0.0000 0.0000 2.274935 1.034989 1.727967\n", + "nm-tRNA-Tyr-ATA-chr11-8 0.0000 0.0000 1.137467 1.034989 0.000000\n", + "nm-tRNA-Tyr-GTA-chr1-142 349.5116 491.4282 350.339986 349.826220 448.407495\n", + "nm-tRNA-Tyr-GTA-chr14-8 336.4393 473.6531 391.288816 367.421030 392.248560\n", + "nm-tRNA-Tyr-GTA-chr2-12 0.0000 0.0000 1.137467 1.034989 0.000000\n", + "nm-tRNA-Tyr-GTA-chr21-2 362.5839 524.8871 386.738946 374.665951 433.719773\n", + " HEK293T.9 HEPG2 HS707A K562\n", + "nm-tRNA-SerTGA-AGA-chr11-7 0.8979098 2.9351469 0.0000 2.4152391\n", + "nm-tRNA-Tyr-ATA-chr11-8 0.0000000 0.0000000 0.0000 0.8050797\n", + "nm-tRNA-Tyr-GTA-chr1-142 379.8158322 391.3529244 409.7049 550.6745203\n", + "nm-tRNA-Tyr-GTA-chr14-8 393.2844788 350.2608673 406.5289 587.7081869\n", + "nm-tRNA-Tyr-GTA-chr2-12 0.0000000 0.9783823 0.0000 0.0000000\n", + "nm-tRNA-Tyr-GTA-chr21-2 394.1823885 386.4610128 358.8888 576.4370709\n", + " LNCaP LS174T MCF7 MDA231\n", + "nm-tRNA-SerTGA-AGA-chr11-7 0.8155154 3.4873 3.844916 0.8983807\n", + "nm-tRNA-Tyr-ATA-chr11-8 1.6310308 0.0000 0.000000 0.0000000\n", + "nm-tRNA-Tyr-GTA-chr1-142 274.8286858 469.6230 799.742572 338.6895331\n", + "nm-tRNA-Tyr-GTA-chr14-8 262.5959549 470.7855 829.540673 335.0960102\n", + "nm-tRNA-Tyr-GTA-chr2-12 0.8155154 0.0000 0.000000 0.0000000\n", + "nm-tRNA-Tyr-GTA-chr21-2 238.9460087 405.6892 834.346818 353.0636247\n", + " MDA453 PACA2 PANC1 PC3 SW480u\n", + "nm-tRNA-SerTGA-AGA-chr11-7 5.483139 0.0000 1.282899 0.0000 0.8380149\n", + "nm-tRNA-Tyr-ATA-chr11-8 0.000000 0.0000 0.000000 0.0000 0.0000000\n", + "nm-tRNA-Tyr-GTA-chr1-142 418.546244 475.7318 306.612814 380.8959 374.5926481\n", + "nm-tRNA-Tyr-GTA-chr14-8 441.392655 507.2074 310.461510 435.1252 382.9727968\n", + "nm-tRNA-Tyr-GTA-chr2-12 0.000000 0.0000 0.000000 0.0000 0.8380149\n", + "nm-tRNA-Tyr-GTA-chr21-2 425.857096 482.0269 302.764117 393.8077 390.5149306\n", + " SW620u ZR751\n", + "nm-tRNA-SerTGA-AGA-chr11-7 0.9703089 0.0000\n", + "nm-tRNA-Tyr-ATA-chr11-8 0.0000000 0.0000\n", + "nm-tRNA-Tyr-GTA-chr1-142 594.7993350 377.6161\n", + "nm-tRNA-Tyr-GTA-chr14-8 635.5523074 382.4112\n", + "nm-tRNA-Tyr-GTA-chr2-12 0.0000000 0.0000\n", + "nm-tRNA-Tyr-GTA-chr21-2 616.1461301 401.5917\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "%%R\n", + "library(DESeq2)\n", + "colData <- data.frame(cond=colnames(m), row.names=colnames(m))\n", + "dds <- DESeqDataSetFromMatrix(countData = m, colData=colData, design = ~ cond)\n", + "sizeFactors(dds) <- sf\n", + "ncu <- counts(dds, normalized=TRUE)\n", + "head(ncu)" + ] + }, + { + "cell_type": "code", + "execution_count": 79, + "metadata": {}, + "outputs": [], + "source": [ + "%%R\n", + "write.table(m, file=\"tRF_counts.txt\", sep=\"\\t\", quote=FALSE, col.names=NA )\n", + "write.table(ncu, file=\"tRF_norm-counts.txt\", sep=\"\\t\", quote=FALSE, col.names=NA )" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/smRNA-seq/count/A2508.srt.dd.q10.oncRNA.cnt b/smRNA-seq/count/A2508.srt.dd.q10.oncRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..6da93858c166282cb6e0703819685200f8c5d257 --- /dev/null +++ b/smRNA-seq/count/A2508.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,344 @@ +chr10:103367799-103367828:- 1 +chr10:110229456-110229486:+ 1 +chr10:11165800-11165858:- 1 +chr10:130190374-130190405:+ 1 +chr10:15169088-15169116:+ 1 +chr10:70815902-70815930:+ 1 +chr10:71981555-71981651:- 1 +chr10:77711544-77711577:- 1 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b/smRNA-seq/count/A375.hsa-miR.cnt new file mode 100644 index 0000000000000000000000000000000000000000..9deace2d394a8eb703f9d95cf8c8a7a49a115aad --- /dev/null +++ b/smRNA-seq/count/A375.hsa-miR.cnt @@ -0,0 +1,283 @@ +hsa-let-7a-2-3p 9 +hsa-let-7a-3p 65 +hsa-let-7a-5p 843 +hsa-let-7b-3p 12 +hsa-let-7b-5p 195 +hsa-let-7c-5p 11 +hsa-let-7d-3p 7 +hsa-let-7d-5p 45 +hsa-let-7e-3p 6 +hsa-let-7e-5p 95 +hsa-let-7f-1-3p 3 +hsa-let-7f-2-3p 14 +hsa-let-7f-5p 386 +hsa-let-7g-3p 1 +hsa-let-7g-5p 441 +hsa-let-7i-3p 56 +hsa-let-7i-5p 449 +hsa-miR-100-3p 11 +hsa-miR-100-5p 92 +hsa-miR-101-3p 2 +hsa-miR-101-5p 1 +hsa-miR-10399-5p 1 +hsa-miR-105-5p 1 +hsa-miR-106b-3p 9 +hsa-miR-106b-5p 4 +hsa-miR-10a-3p 2 +hsa-miR-10a-5p 4 +hsa-miR-10b-3p 1 +hsa-miR-10b-5p 1 +hsa-miR-1180-5p 1 +hsa-miR-12130 1 +hsa-miR-12136 4 +hsa-miR-1246 21 +hsa-miR-125a-3p 1 +hsa-miR-125a-5p 234 +hsa-miR-125b-1-3p 3 +hsa-miR-125b-5p 147 +hsa-miR-1260b 61 +hsa-miR-1261 1 +hsa-miR-126-5p 2 +hsa-miR-1275 23 +hsa-miR-1278 1 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a/smRNA-seq/count/A549.srt.dd.q10.oncRNA.cnt b/smRNA-seq/count/A549.srt.dd.q10.oncRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..8274c7e99c36db04f67f8ff08497263e1e635573 --- /dev/null +++ b/smRNA-seq/count/A549.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,288 @@ +chr10:103367799-103367828:- 1 +chr10:110601853-110601885:+ 1 +chr10:113045362-113045392:+ 2 +chr10:119596863-119596893:- 1 +chr10:124791951-124791980:+ 2 +chr10:125161314-125161342:+ 1 +chr10:133520411-133520464:+ 1 +chr10:134966-134992:+ 1 +chr10:21524991-21525125:- 1 +chr10:4678115-4678219:- 1 +chr10:5291926-5292086:+ 1 +chr10:60784710-60784793:+ 1 +chr10:70478580-70478612:- 1 +chr10:70815902-70815930:+ 1 +chr10:73874728-73874756:+ 1 +chr10:78033458-78033641:- 1 +chr10:94545630-94545654:- 1 +chr10:94607752-94607868:+ 1 +chr1:100352312-100352352:- 1 +chr1:106435350-106435445:- 1 +chr11:13009096-13009126:- 1 +chr11:1764075-1764105:+ 1 +chr11:31370061-31370203:- 1 +chr11:35214888-35214920:+ 1 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+tRNA-Val-CAC-2-1 349 +tRNA-Val-CAC-3-1 957 +tRNA-Val-CAC-4-1 604 +tRNA-Val-CAC-5-1 296 +tRNA-Val-CAC-6-1 2 +tRNA-Val-CAC-7-1 1 +tRNA-Val-CAC-8-1 12 +tRNA-Val-CAC-9-1 36 +tRNA-Val-CAC-chr1-134 1 +tRNA-Val-CAC-chr1-136 20 +tRNA-Val-CAC-chr1-16 349 +tRNA-Val-CAC-chr1-93 339 +tRNA-Val-TAC-1-1 1141 +tRNA-Val-TAC-1-2 1339 +tRNA-Val-TAC-2-1 2038 +tRNA-Val-TAC-3-1 856 +tRNA-Val-TAC-4-1 133 +tRNA-Val-TAC-chr17-24 1 diff --git a/smRNA-seq/count/BxPC3.hsa-miR.cnt b/smRNA-seq/count/BxPC3.hsa-miR.cnt new file mode 100644 index 0000000000000000000000000000000000000000..6a5495f0861babaa0adc1addde5261de5642da28 --- /dev/null +++ b/smRNA-seq/count/BxPC3.hsa-miR.cnt @@ -0,0 +1,296 @@ +hsa-let-7a-3p 32 +hsa-let-7a-5p 894 +hsa-let-7b-3p 22 +hsa-let-7b-5p 306 +hsa-let-7c-5p 4 +hsa-let-7d-3p 2 +hsa-let-7d-5p 19 +hsa-let-7e-3p 3 +hsa-let-7e-5p 144 +hsa-let-7f-1-3p 2 +hsa-let-7f-2-3p 8 +hsa-let-7f-5p 446 +hsa-let-7g-5p 225 +hsa-let-7i-3p 19 +hsa-let-7i-5p 86 +hsa-miR-100-3p 2 +hsa-miR-100-5p 29 +hsa-miR-106b-3p 2 +hsa-miR-106b-5p 2 +hsa-miR-10a-3p 4 +hsa-miR-10a-5p 28 +hsa-miR-10b-3p 1 +hsa-miR-10b-5p 2 +hsa-miR-1180-5p 2 +hsa-miR-1185-1-3p 5 +hsa-miR-1185-5p 1 +hsa-miR-12136 4 +hsa-miR-1226-3p 3 +hsa-miR-1246 15 +hsa-miR-125a-3p 1 +hsa-miR-125a-5p 158 +hsa-miR-125b-1-3p 1 +hsa-miR-125b-5p 45 +hsa-miR-1260a 1 +hsa-miR-1260b 63 +hsa-miR-1262 2 +hsa-miR-126-3p 2 +hsa-miR-126-5p 17 +hsa-miR-127-3p 10 +hsa-miR-1275 9 +hsa-miR-1277-3p 1 +hsa-miR-128-3p 23 +hsa-miR-1290 16 +hsa-miR-1304-3p 2 +hsa-miR-1307-3p 1 +hsa-miR-130a-3p 4 +hsa-miR-130a-5p 1 +hsa-miR-130b-3p 4 +hsa-miR-130b-5p 2 +hsa-miR-132-3p 3 +hsa-miR-134-5p 11 +hsa-miR-136-3p 76 +hsa-miR-136-5p 3 +hsa-miR-139-5p 1 +hsa-miR-1-3p 8 +hsa-miR-140-3p 1 +hsa-miR-140-5p 7 +hsa-miR-146a-5p 197 +hsa-miR-146b-5p 2 +hsa-miR-147b-3p 1 +hsa-miR-148a-3p 1 +hsa-miR-148b-3p 4 +hsa-miR-149-5p 12 +hsa-miR-151a-3p 102 +hsa-miR-151a-5p 26 +hsa-miR-153-3p 2 +hsa-miR-154-3p 6 +hsa-miR-15a-3p 1 +hsa-miR-15b-3p 29 +hsa-miR-15b-5p 8 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+tRNA-Trp-CCA-3-1 103 +tRNA-Trp-CCA-3-2 99 +tRNA-Trp-CCA-3-3 120 +tRNA-Trp-CCA-4-1 42 +tRNA-Trp-CCA-5-1 3 +tRNA-Trp-CCA-chr7-31 1 +tRNA-Tyr-GTA-10-1 1 +tRNA-Tyr-GTA-1-1 39 +tRNA-Tyr-GTA-2-1 593 +tRNA-Tyr-GTA-3-1 118 +tRNA-Tyr-GTA-4-1 124 +tRNA-Tyr-GTA-5-1 521 +tRNA-Tyr-GTA-5-2 9 +tRNA-Tyr-GTA-5-3 414 +tRNA-Tyr-GTA-5-4 486 +tRNA-Tyr-GTA-5-5 145 +tRNA-Tyr-GTA-6-1 50 +tRNA-Tyr-GTA-7-1 77 +tRNA-Tyr-GTA-8-1 80 +tRNA-Und-NNN-2-1 1 +tRNA-Und-NNN-3-1 11 +tRNA-Und-NNN-4-1 1 +tRNA-Val-AAC-1-1 226 +tRNA-Val-AAC-1-2 176 +tRNA-Val-AAC-1-3 173 +tRNA-Val-AAC-1-4 181 +tRNA-Val-AAC-1-5 143 +tRNA-Val-AAC-2-1 550 +tRNA-Val-AAC-3-1 354 +tRNA-Val-AAC-4-1 59 +tRNA-Val-AAC-5-1 80 +tRNA-Val-AAC-6-1 341 +tRNA-Val-CAC-1-1 230 +tRNA-Val-CAC-11-2 44 +tRNA-Val-CAC-1-2 345 +tRNA-Val-CAC-1-3 233 +tRNA-Val-CAC-1-4 969 +tRNA-Val-CAC-1-5 352 +tRNA-Val-CAC-1-6 371 +tRNA-Val-CAC-2-1 418 +tRNA-Val-CAC-3-1 923 +tRNA-Val-CAC-4-1 215 +tRNA-Val-CAC-5-1 276 +tRNA-Val-CAC-6-1 144 +tRNA-Val-CAC-7-1 1 +tRNA-Val-CAC-8-1 11 +tRNA-Val-CAC-9-1 192 +tRNA-Val-CAC-chr1-134 2 +tRNA-Val-CAC-chr1-136 44 +tRNA-Val-CAC-chr1-16 368 +tRNA-Val-CAC-chr1-93 249 +tRNA-Val-TAC-1-1 749 +tRNA-Val-TAC-1-2 790 +tRNA-Val-TAC-2-1 2437 +tRNA-Val-TAC-3-1 620 +tRNA-Val-TAC-4-1 280 +U100 28 +U101 184 +U102 1129 +U103 118 +U103B 119 +U104 297 +U105 69 +U105B 161 +U106 1279 +U107 36 +U108 17 +U109 35 +U13 41 +U14A 278 +U14B 22 +U15A 284 +U15B 734 +U16 362 +U17a 293 +U17b 321 +U18A 158 +U18B 1686 +U18C 1025 +U19 212 +U19-2 25 +U20 25 +U21 273 +U22 1612 +U23 784 +U24 80 +U25 273 +U26 824 +U27 1832 +U28 182 +U29 1120 +U3 2621 +U30 1127 +U31 2127 +U3-2 1048 +U32A 307 +U3-2B 990 +U3-3 820 +U33 37 +U3-4 856 +U34 1385 +U35A 84 +U35B 139 +U36A 69 +U36B 204 +U36C 750 +U37 65 +U38A 170 +U38B 925 +U41 8 +U42A 436 +U42B 856 +U43 1888 +U44 2034 +U45A 141 +U45B 37 +U45C 42 +U46 804 +U47 1453 +U48 395 +U49A 1238 +U49B 557 +U50 30 +U50B 221 +U51 271 +U52 2011 +U53 44 +U54 96 +U55 20 +U56 1969 +U57 22 +U58A 612 +U58B 671 +U58C 93 +U59A 822 +U59B 838 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+tRNA-Val-CAC-9-1 192 +tRNA-Val-CAC-chr1-134 2 +tRNA-Val-CAC-chr1-136 44 +tRNA-Val-CAC-chr1-16 368 +tRNA-Val-CAC-chr1-93 249 +tRNA-Val-TAC-1-1 749 +tRNA-Val-TAC-1-2 790 +tRNA-Val-TAC-2-1 2437 +tRNA-Val-TAC-3-1 620 +tRNA-Val-TAC-4-1 280 diff --git a/smRNA-seq/count/C42Bu.hsa-miR.cnt b/smRNA-seq/count/C42Bu.hsa-miR.cnt new file mode 100644 index 0000000000000000000000000000000000000000..8920b932852aa4ff222cd6ab1150d71dfb4b00f0 --- /dev/null +++ b/smRNA-seq/count/C42Bu.hsa-miR.cnt @@ -0,0 +1,239 @@ +hsa-let-7a-3p 66 +hsa-let-7a-5p 1108 +hsa-let-7b-3p 131 +hsa-let-7b-5p 833 +hsa-let-7c-3p 8 +hsa-let-7c-5p 685 +hsa-let-7d-3p 23 +hsa-let-7d-5p 120 +hsa-let-7e-3p 1 +hsa-let-7e-5p 42 +hsa-let-7f-1-3p 8 +hsa-let-7f-2-3p 42 +hsa-let-7f-5p 630 +hsa-let-7g-5p 430 +hsa-let-7i-3p 7 +hsa-let-7i-5p 96 +hsa-miR-100-5p 1 +hsa-miR-101-3p 1 +hsa-miR-106b-3p 2 +hsa-miR-106b-5p 3 +hsa-miR-1180-5p 1 +hsa-miR-12136 4 +hsa-miR-1226-3p 1 +hsa-miR-1246 122 +hsa-miR-1255a 3 +hsa-miR-125a-3p 1 +hsa-miR-125a-5p 55 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b/smRNA-seq/count/C42Bu.srt.annotated.cnt new file mode 100644 index 0000000000000000000000000000000000000000..7a8d953eb3c93d9a1d0e10c56096cb16d907ea54 --- /dev/null +++ b/smRNA-seq/count/C42Bu.srt.annotated.cnt @@ -0,0 +1,1056 @@ +14q(I-5) 1 +ACA1 378 +ACA10 290 +ACA11 23 +ACA12 99 +ACA13 492 +ACA14a 4 +ACA14b 221 +ACA15 64 +ACA16 24 +ACA17 741 +ACA18 412 +ACA19 238 +ACA20 421 +ACA21 1653 +ACA22 12 +ACA23 221 +ACA24 307 +ACA25 498 +ACA26 496 +ACA27 423 +ACA28 181 +ACA2a 32 +ACA2b 47 +ACA3 884 +ACA30 97 +ACA31 349 +ACA3-2 947 +ACA32 279 +ACA33 449 +ACA34 36 +ACA35 45 +ACA36 55 +ACA36B 30 +ACA37 73 +ACA38 49 +ACA39 215 +ACA4 1044 +ACA40 634 +ACA41 88 +ACA42 403 +ACA43 61 +ACA44 255 +ACA45 69 +ACA46 241 +ACA47 11 +ACA48 443 +ACA49 20 +ACA5 171 +ACA50 29 +ACA51 309 +ACA52 95 +ACA53 102 +ACA54 70 +ACA55 258 +ACA56 91 +ACA57 17 +ACA58 388 +ACA59 12 +ACA59B 17 +ACA5c 137 +ACA6 347 +ACA60 88 +ACA61 274 +ACA62 654 +ACA63 7 +ACA64 66 +ACA65 27 +ACA66 31 +ACA67 29 +ACA67B 185 +ACA68 43 +ACA7 267 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+U21 249 +U22 2004 +U23 525 +U24 319 +U25 494 +U26 773 +U27 1558 +U28 120 +U29 1030 +U3 4621 +U30 1023 +U31 2496 +U3-2 1484 +U32A 671 +U3-2B 1250 +U3-3 1129 +U33 65 +U3-4 1139 +U34 2136 +U35A 274 +U35B 681 +U36A 141 +U36B 222 +U36C 1218 +U37 294 +U38A 249 +U38B 1271 +U41 2 +U42A 131 +U42B 750 +U43 2240 +U44 1763 +U45A 375 +U45B 69 +U45C 164 +U46 945 +U47 1202 +U48 534 +U49A 1758 +U49B 749 +U50 14 +U50B 275 +U51 241 +U52 1963 +U53 116 +U54 120 +U55 41 +U56 1458 +U57 29 +U58A 633 +U58B 851 +U58C 129 +U59A 442 +U59B 774 +U60 183 +U61 209 +U62A 726 +U62B 776 +U63 723 +U64 1555 +U65 1170 +U66 351 +U67 420 +U68 869 +U69 374 +U70 395 +U71a 312 +U71b 450 +U71c 197 +U71d 679 +U72 488 +U73a 90 +U74 1236 +U75 1592 +U76 1050 +U77 1605 +U78 338 +U79 1723 +U8 2599 +U80 639 +U81 545 +U82 1452 +U83 502 +U83A 868 +U83B 1473 +U84 864 +U85 35 +U86 44 +U87 18 +U88 3 +U89 4 +U90 1 +U91 1 +U92 58 +U93 8 +U94 61 +U95 818 +U96a 427 +U97 55 +U99 156 +Z17B 691 diff --git 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+tRNA-Glu-TTC-3-1 1275 +tRNA-Glu-TTC-4-2 1926 +tRNA-Glu-TTC-5-1 164 +tRNA-Glu-TTC-8-1 2 +tRNA-Glu-TTC-chr1-138 1800 +tRNA-Gly-CAC-chr1-17 6 +tRNA-Gly-CAC-chr1-94 12 +tRNA-Gly-CCC-1-2 388 +tRNA-Gly-CCC-2-1 480 +tRNA-Gly-CCC-2-2 2460 +tRNA-Gly-CCC-6-1 124 +tRNA-Gly-CCC-7-1 369 +tRNA-Gly-CCC-chr1-135 170 +tRNA-Gly-CCC-chr1-137 438 +tRNA-Gly-CCC-chr1-2 139 +tRNA-Gly-CCC-chr1-33 1 +tRNA-Gly-GCC-1-1 2114 +tRNA-Gly-GCC-1-2 2061 +tRNA-Gly-GCC-1-3 2108 +tRNA-Gly-GCC-1-4 2089 +tRNA-Gly-GCC-1-5 2181 +tRNA-Gly-GCC-2-1 2873 +tRNA-Gly-GCC-2-2 1440 +tRNA-Gly-GCC-2-3 2378 +tRNA-Gly-GCC-2-4 2244 +tRNA-Gly-GCC-2-5 2509 +tRNA-Gly-GCC-2-6 3344 +tRNA-Gly-GCC-3-1 990 +tRNA-Gly-GCC-4-1 4 +tRNA-Gly-GCC-5-1 7 +tRNA-Gly-GCC-6-1 1 +tRNA-Gly-TCC-1-1 1933 +tRNA-Gly-TCC-2-1 1384 +tRNA-Gly-TCC-2-2 1949 +tRNA-Gly-TCC-2-3 1963 +tRNA-Gly-TCC-2-4 1915 +tRNA-Gly-TCC-2-5 2041 +tRNA-Gly-TCC-2-6 1747 +tRNA-Gly-TCC-3-1 4547 +tRNA-Gly-TCC-4-1 16 +tRNA-His-GTG-1-1 2003 +tRNA-His-GTG-1-2 1977 +tRNA-His-GTG-1-3 1943 +tRNA-His-GTG-1-4 2846 +tRNA-His-GTG-1-5 3297 +tRNA-His-GTG-1-6 3149 +tRNA-His-GTG-1-7 2874 +tRNA-His-GTG-1-8 2806 +tRNA-His-GTG-1-9 1944 +tRNA-His-GTG-2-1 10 +tRNA-Ile-AAT-1-1 7 +tRNA-Ile-AAT-2-1 69 +tRNA-Ile-AAT-3-1 74 +tRNA-Ile-AAT-4-1 50 +tRNA-Ile-AAT-5-1 521 +tRNA-Ile-AAT-5-2 132 +tRNA-Ile-AAT-5-3 320 +tRNA-Ile-AAT-5-4 1088 +tRNA-Ile-AAT-5-5 232 +tRNA-Ile-AAT-6-1 38 +tRNA-Ile-AAT-7-1 30 +tRNA-Ile-AAT-7-2 14 +tRNA-Ile-AAT-8-1 281 +tRNA-Ile-AAT-9-1 1 +tRNA-Ile-AAT-chr6-79 19 +tRNA-Ile-GAT-1-1 13 +tRNA-Ile-GAT-1-2 4 +tRNA-Ile-GAT-1-3 7 +tRNA-Ile-TAT-1-1 814 +tRNA-Ile-TAT-2-1 162 +tRNA-Ile-TAT-2-2 101 +tRNA-Ile-TAT-2-3 151 +tRNA-Ile-TAT-3-1 20 +tRNA-iMet-CAT-1-1 707 +tRNA-iMet-CAT-1-2 325 +tRNA-iMet-CAT-1-3 311 +tRNA-iMet-CAT-1-4 235 +tRNA-iMet-CAT-1-5 221 +tRNA-iMet-CAT-1-6 670 +tRNA-iMet-CAT-1-7 149 +tRNA-iMet-CAT-1-8 144 +tRNA-iMet-CAT-2-1 256 +tRNA-iMet-CAT-3-1 1 +tRNA-Leu-AAG-1-1 972 +tRNA-Leu-AAG-1-2 369 +tRNA-Leu-AAG-1-3 933 +tRNA-Leu-AAG-2-1 324 +tRNA-Leu-AAG-2-2 1364 +tRNA-Leu-AAG-2-3 324 +tRNA-Leu-AAG-2-4 525 +tRNA-Leu-AAG-3-1 243 +tRNA-Leu-AAG-4-1 11 +tRNA-Leu-AAG-5-1 1 +tRNA-Leu-AAG-6-1 3 +tRNA-Leu-AAG-7-1 1 +tRNA-Leu-CAA-1-1 270 +tRNA-Leu-CAA-1-2 543 +tRNA-Leu-CAA-2-1 263 +tRNA-Leu-CAA-3-1 62 +tRNA-Leu-CAA-4-1 727 +tRNA-Leu-CAA-5-1 6 +tRNA-Leu-CAA-6-1 60 +tRNA-Leu-CAG-1-1 66 +tRNA-Leu-CAG-1-2 55 +tRNA-Leu-CAG-1-3 85 +tRNA-Leu-CAG-1-4 73 +tRNA-Leu-CAG-1-5 69 +tRNA-Leu-CAG-1-6 812 +tRNA-Leu-CAG-1-7 129 +tRNA-Leu-CAG-2-1 106 +tRNA-Leu-CAG-2-2 692 +tRNA-Leu-CAG-chr9-7 13 +tRNA-Leu-TAA-1-1 262 +tRNA-Leu-TAA-2-1 66 +tRNA-Leu-TAA-3-1 60 +tRNA-Leu-TAA-4-1 34 +tRNA-Leu-TAA-chr11-11 1 +tRNA-Leu-TAG-1-1 1448 +tRNA-Leu-TAG-2-1 942 +tRNA-Leu-TAG-3-1 1936 +tRNA-Lys-CTT-10-1 1 +tRNA-Lys-CTT-1-1 3044 +tRNA-Lys-CTT-11-1 382 +tRNA-Lys-CTT-1-2 2827 +tRNA-Lys-CTT-13-1 1 +tRNA-Lys-CTT-14-1 7 +tRNA-Lys-CTT-2-1 1794 +tRNA-Lys-CTT-2-2 2226 +tRNA-Lys-CTT-2-3 1942 +tRNA-Lys-CTT-2-4 2205 +tRNA-Lys-CTT-2-5 1612 +tRNA-Lys-CTT-3-1 165 +tRNA-Lys-CTT-4-1 1014 +tRNA-Lys-CTT-5-1 251 +tRNA-Lys-CTT-6-1 82 +tRNA-Lys-CTT-7-1 6 +tRNA-Lys-CTT-9-1 4 +tRNA-Lys-CTT-chr15-5 106 +tRNA-Lys-CTT-chr7-30 35 +tRNA-Lys-TTT-10-1 3 +tRNA-Lys-TTT-1-1 135 +tRNA-Lys-TTT-11-1 1 +tRNA-Lys-TTT-13-1 22 +tRNA-Lys-TTT-14-1 19 +tRNA-Lys-TTT-15-1 1 +tRNA-Lys-TTT-2-1 140 +tRNA-Lys-TTT-3-1 1870 +tRNA-Lys-TTT-3-2 887 +tRNA-Lys-TTT-3-3 670 +tRNA-Lys-TTT-3-4 682 +tRNA-Lys-TTT-3-5 643 +tRNA-Lys-TTT-4-1 518 +tRNA-Lys-TTT-5-1 337 +tRNA-Lys-TTT-6-1 193 +tRNA-Lys-TTT-7-1 997 +tRNA-Lys-TTT-8-1 3 +tRNA-Lys-TTT-9-1 37 +tRNA-Met-CAT-1-1 1727 +tRNA-Met-CAT-2-1 29 +tRNA-Met-CAT-3-1 316 +tRNA-Met-CAT-3-2 3597 +tRNA-Met-CAT-4-1 299 +tRNA-Met-CAT-4-2 244 +tRNA-Met-CAT-4-3 248 +tRNA-Met-CAT-5-1 3 +tRNA-Met-CAT-6-1 99 +tRNA-Met-CAT-7-1 1 +tRNA-Met-CAT-chr6-167 18 +tRNA-Met-CAT-chr6-80 4 +tRNA-Phe-GAA-10-1 4 +tRNA-Phe-GAA-1-1 103 +tRNA-Phe-GAA-1-2 56 +tRNA-Phe-GAA-1-3 102 +tRNA-Phe-GAA-1-4 175 +tRNA-Phe-GAA-1-5 148 +tRNA-Phe-GAA-1-6 37 +tRNA-Phe-GAA-2-1 85 +tRNA-Phe-GAA-3-1 455 +tRNA-Phe-GAA-4-1 17 +tRNA-Phe-GAA-5-1 9 +tRNA-Phe-GAA-6-1 17 +tRNA-Phe-GAA-7-1 1 +tRNA-Phe-GAA-8-1 2 +tRNA-Phe-GAA-9-1 7 +tRNA-Pro-AGG-1-1 686 +tRNA-Pro-AGG-2-1 437 +tRNA-Pro-AGG-2-2 229 +tRNA-Pro-AGG-2-3 323 +tRNA-Pro-AGG-2-4 666 +tRNA-Pro-AGG-2-5 554 +tRNA-Pro-AGG-2-6 433 +tRNA-Pro-AGG-2-7 562 +tRNA-Pro-AGG-2-8 317 +tRNA-Pro-AGG-3-1 1 +tRNA-Pro-CGG-1-1 1212 +tRNA-Pro-CGG-1-2 922 +tRNA-Pro-CGG-1-3 1885 +tRNA-Pro-CGG-2-1 2067 +tRNA-Pro-TGG-1-1 1057 +tRNA-Pro-TGG-2-1 2459 +tRNA-Pro-TGG-3-1 1422 +tRNA-Pro-TGG-3-2 510 +tRNA-Pro-TGG-3-3 554 +tRNA-Pro-TGG-3-4 5226 +tRNA-Pro-TGG-3-5 4413 +tRNA-SeC-TCA-1-1 3752 +tRNA-SeC-TCA-2-1 50 +tRNA-Ser-ACT-1-1 198 +tRNA-Ser-AGA-1-1 131 +tRNA-Ser-AGA-2-1 232 +tRNA-Ser-AGA-2-2 134 +tRNA-Ser-AGA-2-3 116 +tRNA-Ser-AGA-2-4 122 +tRNA-Ser-AGA-2-5 121 +tRNA-Ser-AGA-2-6 206 +tRNA-Ser-AGA-3-1 128 +tRNA-Ser-AGA-4-1 119 +tRNA-Ser-CGA-1-1 757 +tRNA-Ser-CGA-2-1 569 +tRNA-Ser-CGA-3-1 1261 +tRNA-Ser-CGA-4-1 252 +tRNA-Ser-GCT-1-1 79 +tRNA-Ser-GCT-2-1 250 +tRNA-Ser-GCT-3-1 727 +tRNA-Ser-GCT-4-1 816 +tRNA-Ser-GCT-4-2 1043 +tRNA-Ser-GCT-4-3 262 +tRNA-Ser-GCT-5-1 273 +tRNA-Ser-GCT-6-1 305 +tRNA-Ser-TGA-1-1 260 +tRNA-Ser-TGA-2-1 441 +tRNA-Ser-TGA-3-1 392 +tRNA-Ser-TGA-4-1 343 +tRNA-Thr-AGT-1-1 375 +tRNA-Thr-AGT-1-2 31 +tRNA-Thr-AGT-1-3 77 +tRNA-Thr-AGT-2-1 36 +tRNA-Thr-AGT-2-2 35 +tRNA-Thr-AGT-3-1 56 +tRNA-Thr-AGT-4-1 40 +tRNA-Thr-AGT-5-1 16 +tRNA-Thr-AGT-6-1 12 +tRNA-Thr-CGT-1-1 13 +tRNA-Thr-CGT-2-1 179 +tRNA-Thr-CGT-3-1 43 +tRNA-Thr-CGT-4-1 195 +tRNA-Thr-CGT-5-1 97 +tRNA-Thr-CGT-6-1 326 +tRNA-Thr-TGT-1-1 33 +tRNA-Thr-TGT-2-1 145 +tRNA-Thr-TGT-3-1 281 +tRNA-Thr-TGT-4-1 532 +tRNA-Thr-TGT-5-1 185 +tRNA-Thr-TGT-6-1 432 +tRNA-Trp-CCA-1-1 70 +tRNA-Trp-CCA-2-1 245 +tRNA-Trp-CCA-3-1 36 +tRNA-Trp-CCA-3-2 99 +tRNA-Trp-CCA-3-3 229 +tRNA-Trp-CCA-4-1 51 +tRNA-Trp-CCA-5-1 2 +tRNA-Trp-CCA-chr7-31 1 +tRNA-Tyr-GTA-1-1 186 +tRNA-Tyr-GTA-2-1 808 +tRNA-Tyr-GTA-3-1 113 +tRNA-Tyr-GTA-4-1 111 +tRNA-Tyr-GTA-5-1 344 +tRNA-Tyr-GTA-5-2 41 +tRNA-Tyr-GTA-5-3 326 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0000000000000000000000000000000000000000..e1a9553f6a0376dee73cd8e567cc08ba363a1fbf --- /dev/null +++ b/smRNA-seq/count/Colo320.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,475 @@ +chr10:102450480-102450516:- 1 +chr10:104232484-104232640:+ 1 +chr10:110003784-110003896:+ 2 +chr10:113045362-113045392:+ 1 +chr10:114975591-114975675:+ 1 +chr10:121974791-121974818:- 1 +chr10:123154880-123154910:+ 1 +chr10:129808414-129808463:+ 1 +chr10:15169088-15169116:+ 1 +chr10:22230482-22230578:- 1 +chr10:28620900-28620931:+ 1 +chr10:28678292-28678322:+ 1 +chr10:32022971-32023003:- 1 +chr10:6113474-6113511:+ 1 +chr10:70478580-70478612:- 1 +chr10:70815902-70815930:+ 1 +chr10:72261542-72261569:- 1 +chr10:89645490-89645534:- 1 +chr10:92351723-92351753:+ 1 +chr10:99423714-99423777:- 1 +chr1:109042406-109042438:+ 1 +chr11:118252217-118252246:+ 1 +chr11:125655734-125655765:+ 1 +chr1:112707236-112707287:+ 1 +chr1:117366843-117366872:+ 2 +chr11:1764075-1764105:+ 4 +chr11:23349292-23349325:- 1 +chr11:33161646-33161674:+ 1 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114 +tRNA-Cys-GCA-23-1 6 +tRNA-Cys-GCA-2-4 333 +tRNA-Cys-GCA-24-1 2 +tRNA-Cys-GCA-25-1 1 +tRNA-Cys-GCA-3-1 2 +tRNA-Cys-GCA-4-1 144 +tRNA-Cys-GCA-5-1 26 +tRNA-Cys-GCA-6-1 34 +tRNA-Cys-GCA-7-1 19 +tRNA-Cys-GCA-8-1 27 +tRNA-Cys-GCA-9-1 5 +tRNA-Cys-GCA-9-2 10 +tRNA-Cys-GCA-9-3 11 +tRNA-Cys-GCA-9-4 8 +tRNA-Gln-CTG-10-1 2 +tRNA-Gln-CTG-1-1 5615 +tRNA-Gln-CTG-11-1 1 +tRNA-Gln-CTG-1-2 5480 +tRNA-Gln-CTG-12-1 4 +tRNA-Gln-CTG-1-3 5893 +tRNA-Gln-CTG-1-4 8062 +tRNA-Gln-CTG-1-5 6117 +tRNA-Gln-CTG-2-1 7225 +tRNA-Gln-CTG-3-1 639 +tRNA-Gln-CTG-3-2 649 +tRNA-Gln-CTG-4-1 375 +tRNA-Gln-CTG-4-2 365 +tRNA-Gln-CTG-5-1 489 +tRNA-Gln-CTG-6-1 952 +tRNA-Gln-CTG-7-1 14 +tRNA-Gln-CTG-8-1 23 +tRNA-Gln-CTG-8-2 9 +tRNA-Gln-CTG-chr1-130 11 +tRNA-Gln-CTG-chr1-23 12 +tRNA-Gln-TTG-1-1 2413 +tRNA-Gln-TTG-2-1 417 +tRNA-Gln-TTG-3-1 1211 +tRNA-Gln-TTG-3-2 1215 +tRNA-Gln-TTG-3-3 1144 +tRNA-Gln-TTG-4-1 13 +tRNA-Gln-TTG-6-1 6 +tRNA-Glu-CTC-1-1 4661 +tRNA-Glu-CTC-1-2 5249 +tRNA-Glu-CTC-1-3 5442 +tRNA-Glu-CTC-1-4 5296 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3383 +tRNA-Lys-CTT-2-2 3508 +tRNA-Lys-CTT-2-3 3737 +tRNA-Lys-CTT-2-4 3138 +tRNA-Lys-CTT-2-5 3050 +tRNA-Lys-CTT-3-1 272 +tRNA-Lys-CTT-4-1 1243 +tRNA-Lys-CTT-5-1 69 +tRNA-Lys-CTT-6-1 294 +tRNA-Lys-CTT-7-1 24 +tRNA-Lys-CTT-9-1 10 +tRNA-Lys-CTT-chr15-5 196 +tRNA-Lys-CTT-chr7-30 52 +tRNA-Lys-TTT-10-1 2 +tRNA-Lys-TTT-1-1 218 +tRNA-Lys-TTT-11-1 1 +tRNA-Lys-TTT-13-1 2 +tRNA-Lys-TTT-14-1 182 +tRNA-Lys-TTT-15-1 1 +tRNA-Lys-TTT-2-1 139 +tRNA-Lys-TTT-3-1 1617 +tRNA-Lys-TTT-3-2 857 +tRNA-Lys-TTT-3-3 646 +tRNA-Lys-TTT-3-4 793 +tRNA-Lys-TTT-3-5 900 +tRNA-Lys-TTT-4-1 417 +tRNA-Lys-TTT-5-1 306 +tRNA-Lys-TTT-6-1 272 +tRNA-Lys-TTT-7-1 33 +tRNA-Lys-TTT-8-1 3 +tRNA-Lys-TTT-9-1 2 +tRNA-Met-CAT-1-1 2642 +tRNA-Met-CAT-2-1 14 +tRNA-Met-CAT-3-1 140 +tRNA-Met-CAT-3-2 540 +tRNA-Met-CAT-4-1 68 +tRNA-Met-CAT-4-2 48 +tRNA-Met-CAT-4-3 36 +tRNA-Met-CAT-6-1 1107 +tRNA-Met-CAT-7-1 13 +tRNA-Met-CAT-chr6-167 4 +tRNA-Phe-GAA-10-1 23 +tRNA-Phe-GAA-1-1 121 +tRNA-Phe-GAA-1-2 85 +tRNA-Phe-GAA-1-3 93 +tRNA-Phe-GAA-1-4 329 +tRNA-Phe-GAA-1-5 352 +tRNA-Phe-GAA-1-6 91 +tRNA-Phe-GAA-2-1 152 +tRNA-Phe-GAA-3-1 163 +tRNA-Phe-GAA-4-1 13 +tRNA-Phe-GAA-5-1 23 +tRNA-Phe-GAA-6-1 3 +tRNA-Phe-GAA-8-1 1 +tRNA-Phe-GAA-9-1 17 +tRNA-Pro-AGG-1-1 334 +tRNA-Pro-AGG-2-1 434 +tRNA-Pro-AGG-2-2 245 +tRNA-Pro-AGG-2-3 295 +tRNA-Pro-AGG-2-4 579 +tRNA-Pro-AGG-2-5 577 +tRNA-Pro-AGG-2-6 554 +tRNA-Pro-AGG-2-7 516 +tRNA-Pro-AGG-2-8 310 +tRNA-Pro-CGG-1-1 1246 +tRNA-Pro-CGG-1-2 1100 +tRNA-Pro-CGG-1-3 1798 +tRNA-Pro-CGG-2-1 1690 +tRNA-Pro-TGG-1-1 1132 +tRNA-Pro-TGG-2-1 3055 +tRNA-Pro-TGG-3-1 1483 +tRNA-Pro-TGG-3-2 608 +tRNA-Pro-TGG-3-3 570 +tRNA-Pro-TGG-3-4 4643 +tRNA-Pro-TGG-3-5 3439 +tRNA-SeC-TCA-1-1 7070 +tRNA-SeC-TCA-2-1 150 +tRNA-Ser-ACT-1-1 227 +tRNA-Ser-AGA-1-1 187 +tRNA-Ser-AGA-2-1 244 +tRNA-Ser-AGA-2-2 148 +tRNA-Ser-AGA-2-3 163 +tRNA-Ser-AGA-2-4 142 +tRNA-Ser-AGA-2-5 128 +tRNA-Ser-AGA-2-6 207 +tRNA-Ser-AGA-3-1 125 +tRNA-Ser-AGA-4-1 241 +tRNA-Ser-AGA-5-1 2 +tRNA-Ser-AGA-6-1 8 +tRNA-Ser-CGA-1-1 575 +tRNA-Ser-CGA-2-1 469 +tRNA-Ser-CGA-3-1 1294 +tRNA-Ser-CGA-4-1 663 +tRNA-Ser-GCT-1-1 31 +tRNA-Ser-GCT-2-1 136 +tRNA-Ser-GCT-3-1 577 +tRNA-Ser-GCT-4-1 635 +tRNA-Ser-GCT-4-2 979 +tRNA-Ser-GCT-4-3 162 +tRNA-Ser-GCT-5-1 152 +tRNA-Ser-GCT-6-1 248 +tRNA-Ser-TGA-1-1 213 +tRNA-Ser-TGA-2-1 268 +tRNA-Ser-TGA-3-1 325 +tRNA-Ser-TGA-4-1 135 +tRNA-Thr-AGT-1-1 303 +tRNA-Thr-AGT-1-2 15 +tRNA-Thr-AGT-1-3 147 +tRNA-Thr-AGT-2-1 19 +tRNA-Thr-AGT-2-2 11 +tRNA-Thr-AGT-3-1 5 +tRNA-Thr-AGT-4-1 6 +tRNA-Thr-AGT-5-1 4 +tRNA-Thr-AGT-6-1 24 +tRNA-Thr-CGT-1-1 5 +tRNA-Thr-CGT-2-1 276 +tRNA-Thr-CGT-3-1 19 +tRNA-Thr-CGT-4-1 186 +tRNA-Thr-CGT-5-1 14 +tRNA-Thr-CGT-6-1 54 +tRNA-Thr-TGT-1-1 27 +tRNA-Thr-TGT-2-1 133 +tRNA-Thr-TGT-3-1 977 +tRNA-Thr-TGT-4-1 1124 +tRNA-Thr-TGT-5-1 276 +tRNA-Thr-TGT-6-1 515 +tRNA-Trp-CCA-1-1 59 +tRNA-Trp-CCA-2-1 301 +tRNA-Trp-CCA-3-1 16 +tRNA-Trp-CCA-3-2 46 +tRNA-Trp-CCA-3-3 150 +tRNA-Trp-CCA-4-1 33 +tRNA-Tyr-GTA-1-1 85 +tRNA-Tyr-GTA-2-1 1697 +tRNA-Tyr-GTA-3-1 13 +tRNA-Tyr-GTA-4-1 34 +tRNA-Tyr-GTA-5-1 583 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b/smRNA-seq/count/H1299.srt.dd.q10.oncRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..ffe0a74996f21f932e3332c7a4567d4e0502848d --- /dev/null +++ b/smRNA-seq/count/H1299.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,387 @@ +chr10:11894620-11894718:- 2 +chr10:119873173-119873202:+ 1 +chr10:119892686-119892712:+ 1 +chr10:130111350-130111398:+ 1 +chr10:13894523-13894556:- 1 +chr10:21533874-21533902:- 1 +chr10:27240566-27240596:- 1 +chr10:32958354-32958383:+ 1 +chr10:38011183-38011215:+ 1 +chr10:43436961-43436990:- 1 +chr10:72319909-72319934:+ 1 +chr10:73783268-73783298:+ 1 +chr10:99732246-99732275:+ 1 +chr11:119097108-119097295:- 1 +chr1:112376233-112376281:- 4 +chr1:113905349-113905380:+ 1 +chr1:117059813-117059844:- 1 +chr11:2891533-2891602:+ 1 +chr11:35140148-35140177:+ 1 +chr11:355961-355990:- 1 +chr1:144552216-144552266:+ 1 +chr1:155324573-155324602:+ 1 +chr1:15542158-15542189:+ 7 +chr1:15542197-15542228:+ 7 +chr1:155479247-155479278:- 1 +chr11:561687-561718:+ 1 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68 +tRNA-Val-CAC-chr1-93 117 +tRNA-Val-TAC-1-1 358 +tRNA-Val-TAC-1-2 540 +tRNA-Val-TAC-2-1 1477 +tRNA-Val-TAC-3-1 334 +tRNA-Val-TAC-4-1 32 diff --git a/smRNA-seq/count/H23u.srt.annotated.cnt b/smRNA-seq/count/H23u.srt.annotated.cnt new file mode 100644 index 0000000000000000000000000000000000000000..8bad6a2effbe8f28550f50619f44d00111dc4ca1 --- /dev/null +++ b/smRNA-seq/count/H23u.srt.annotated.cnt @@ -0,0 +1,1161 @@ +14q(0) 105 +14q(I-3) 61 +14q(I-4) 31 +14q(I-5) 65 +14q(I-6) 46 +14q(I-7) 84 +14q(I-8) 79 +14q(I-9) 50 +14q(II-1) 11 +14q(II-10) 1 +14q(II-11) 1 +14q(II-12) 94 +14q(II-13) 11 +14q(II-14) 2 +14q(II-15) 2 +14q(II-17) 30 +14q(II-20) 18 +14q(II-21) 7 +14q(II-22) 26 +14q(II-23) 5 +14q(II-24) 1 +14q(II-25) 33 +14q(II-26) 2 +14q(II-28) 13 +14q(II-3) 8 +14q(II-9) 8 +ACA1 187 +ACA10 105 +ACA11 12 +ACA12 64 +ACA13 403 +ACA14a 14 +ACA14b 122 +ACA15 29 +ACA16 23 +ACA17 422 +ACA18 231 +ACA19 184 +ACA20 390 +ACA21 1365 +ACA22 18 +ACA23 175 +ACA24 81 +ACA25 228 +ACA26 1047 +ACA27 155 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0000000000000000000000000000000000000000..2ea2e25c18c306681a11e38696fe5c25271ed275 --- /dev/null +++ b/smRNA-seq/count/H23u.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,293 @@ +chr10:27240695-27240725:- 1 +chr10:29142629-29142734:+ 1 +chr10:31603453-31603479:- 1 +chr10:69994325-69994440:- 1 +chr10:70815902-70815930:+ 1 +chr10:87094970-87094999:- 1 +chr10:93893953-93893983:+ 1 +chr1:100917976-100918038:+ 1 +chr11:117144113-117144140:- 1 +chr11:118899210-118899249:- 1 +chr11:123609762-123609793:+ 1 +chr1:112707236-112707287:+ 1 +chr11:130001748-130001776:+ 1 +chr11:130001784-130001813:+ 1 +chr1:114716725-114716756:- 1 +chr1:114717933-114717963:- 1 +chr1:11654882-11654909:+ 1 +chr1:119912282-119912339:- 1 +chr11:2130653-2130682:- 1 +chr11:2139123-2139157:- 1 +chr11:31509852-31509882:+ 1 +chr11:45231511-45231541:+ 1 +chr1:147670848-147670948:- 1 +chr1:150549164-150549193:+ 1 +chr1:150578192-150578350:+ 1 +chr1:155000131-155000161:- 1 +chr1:155227446-155227476:- 1 +chr1:15542158-15542189:+ 11 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0000000000000000000000000000000000000000..b98609894c333a59dca53bedde3e9083f2ae9dd9 --- /dev/null +++ b/smRNA-seq/count/HCT116.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,320 @@ +chr10:102450480-102450516:- 1 +chr10:112375214-112375273:+ 1 +chr10:113045362-113045392:+ 2 +chr10:11684826-11684854:- 1 +chr10:119842553-119842584:- 1 +chr10:119892686-119892712:+ 1 +chr10:18659524-18659551:+ 1 +chr10:43362464-43362491:+ 1 +chr10:43436961-43436990:- 1 +chr10:48523506-48523564:+ 1 +chr10:61903754-61903782:- 1 +chr10:70478580-70478612:- 1 +chr10:70815902-70815930:+ 1 +chr10:78033458-78033641:- 1 +chr10:99732246-99732275:+ 1 +chr1:11059828-11059883:- 1 +chr11:110430155-110430191:+ 1 +chr11:117144113-117144140:- 1 +chr11:117816229-117816297:- 1 +chr11:118897679-118897709:- 1 +chr11:118929536-118929566:- 1 +chr11:122812889-122813028:+ 1 +chr11:125124166-125124283:- 1 +chr11:13711669-13711831:+ 1 +chr11:20574131-20574175:+ 1 +chr1:1206562-1206591:- 1 +chr1:144552216-144552266:+ 1 +chr11:45923030-45923061:+ 2 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411 +tRNA-Pro-AGG-2-4 619 +tRNA-Pro-AGG-2-5 751 +tRNA-Pro-AGG-2-6 597 +tRNA-Pro-AGG-2-7 700 +tRNA-Pro-AGG-2-8 384 +tRNA-Pro-AGG-3-1 3 +tRNA-Pro-CGG-1-1 1357 +tRNA-Pro-CGG-1-2 1106 +tRNA-Pro-CGG-1-3 1752 +tRNA-Pro-CGG-2-1 1395 +tRNA-Pro-TGG-1-1 517 +tRNA-Pro-TGG-2-1 2038 +tRNA-Pro-TGG-3-1 1574 +tRNA-Pro-TGG-3-2 742 +tRNA-Pro-TGG-3-3 649 +tRNA-Pro-TGG-3-4 3951 +tRNA-Pro-TGG-3-5 3067 +tRNA-SeC-TCA-1-1 2613 +tRNA-SeC-TCA-2-1 31 +tRNA-Ser-ACT-1-1 225 +tRNA-Ser-AGA-1-1 101 +tRNA-Ser-AGA-2-1 124 +tRNA-Ser-AGA-2-2 65 +tRNA-Ser-AGA-2-3 72 +tRNA-Ser-AGA-2-4 63 +tRNA-Ser-AGA-2-5 93 +tRNA-Ser-AGA-2-6 140 +tRNA-Ser-AGA-3-1 64 +tRNA-Ser-AGA-4-1 162 +tRNA-Ser-AGA-5-1 12 +tRNA-Ser-CGA-1-1 567 +tRNA-Ser-CGA-2-1 483 +tRNA-Ser-CGA-3-1 1295 +tRNA-Ser-CGA-4-1 391 +tRNA-Ser-GCT-1-1 45 +tRNA-Ser-GCT-2-1 145 +tRNA-Ser-GCT-3-1 456 +tRNA-Ser-GCT-4-1 702 +tRNA-Ser-GCT-4-2 780 +tRNA-Ser-GCT-4-3 151 +tRNA-Ser-GCT-5-1 344 +tRNA-Ser-GCT-6-1 130 +tRNA-Ser-TGA-1-1 131 +tRNA-Ser-TGA-2-1 325 +tRNA-Ser-TGA-3-1 298 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257 +tRNA-Val-AAC-1-3 265 +tRNA-Val-AAC-1-4 261 +tRNA-Val-AAC-1-5 145 +tRNA-Val-AAC-2-1 1089 +tRNA-Val-AAC-3-1 461 +tRNA-Val-AAC-4-1 65 +tRNA-Val-AAC-5-1 73 +tRNA-Val-AAC-6-1 383 +tRNA-Val-CAC-1-1 254 +tRNA-Val-CAC-11-2 21 +tRNA-Val-CAC-1-2 378 +tRNA-Val-CAC-1-3 223 +tRNA-Val-CAC-1-4 721 +tRNA-Val-CAC-1-5 558 +tRNA-Val-CAC-1-6 413 +tRNA-Val-CAC-2-1 614 +tRNA-Val-CAC-3-1 988 +tRNA-Val-CAC-4-1 665 +tRNA-Val-CAC-5-1 382 +tRNA-Val-CAC-6-1 10 +tRNA-Val-CAC-7-1 1 +tRNA-Val-CAC-8-1 33 +tRNA-Val-CAC-9-1 30 +tRNA-Val-CAC-chr1-134 1 +tRNA-Val-CAC-chr1-136 25 +tRNA-Val-CAC-chr1-16 603 +tRNA-Val-CAC-chr1-93 464 +tRNA-Val-TAC-1-1 587 +tRNA-Val-TAC-1-2 854 +tRNA-Val-TAC-2-1 1483 +tRNA-Val-TAC-3-1 980 +tRNA-Val-TAC-4-1 140 +U100 35 +U101 147 +U102 740 +U103 62 +U103B 76 +U104 179 +U105 42 +U105B 53 +U106 258 +U107 28 +U108 2 +U109 11 +U13 265 +U14A 138 +U14B 10 +U15A 43 +U15B 150 +U16 281 +U17a 44 +U17b 66 +U18A 62 +U18B 1278 +U18C 770 +U19 165 +U19-2 9 +U20 12 +U21 212 +U22 1414 +U23 499 +U24 71 +U25 156 +U26 205 +U27 454 +U28 15 +U29 588 +U3 2367 +U30 399 +U31 1733 +U3-2 788 +U32A 288 +U3-2B 723 +U3-3 601 +U33 20 +U3-4 556 +U34 1064 +U35A 121 +U35B 211 +U36A 30 +U36B 57 +U36C 809 +U37 69 +U38A 79 +U38B 714 +U41 9 +U42A 27 +U42B 616 +U43 1960 +U44 1277 +U45A 147 +U45B 16 +U45C 96 +U46 376 +U47 574 +U48 107 +U49A 1257 +U49B 356 +U50 13 +U50B 347 +U51 224 +U52 1102 +U53 40 +U54 23 +U55 6 +U56 1313 +U57 14 +U58A 137 +U58B 239 +U58C 36 +U59A 109 +U59B 137 +U60 31 +U61 66 +U62A 861 +U62B 836 +U63 489 +U64 1391 +U65 639 +U66 312 +U67 234 +U68 381 +U69 771 +U70 335 +U70B 2 +U71a 79 +U71b 345 +U71c 81 +U71d 372 +U72 411 +U73a 81 +U73b 3 +U74 1161 +U75 1289 +U76 312 +U77 1519 +U78 135 +U79 1124 +U8 2170 +U80 220 +U81 163 +U82 1156 +U83 343 +U83A 693 +U83B 1306 +U84 707 +U85 13 +U86 20 +U87 7 +U88 1 +U89 2 +U92 81 +U94 58 +U95 634 +U96a 444 +U97 25 +U99 20 +Z17B 460 diff --git a/smRNA-seq/count/HEK293T-1.srt.dd.q10.oncRNA.cnt b/smRNA-seq/count/HEK293T-1.srt.dd.q10.oncRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..ba6f05f12b11121e85c118ac27be2069dd3c0b09 --- /dev/null +++ b/smRNA-seq/count/HEK293T-1.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,408 @@ +chr10:102245141-102245170:- 1 +chr10:102245172-102245201:- 1 +chr10:102393965-102393995:- 1 +chr10:113679713-113679741:- 1 +chr10:116609628-116609767:- 1 +chr10:22321239-22321269:+ 1 +chr10:45000941-45000966:+ 1 +chr10:70200174-70200270:- 1 +chr10:70815902-70815930:+ 1 +chr10:77926659-77926689:- 1 +chr10:92593234-92593262:+ 1 +chr10:93893953-93893983:+ 1 +chr10:97425871-97425899:- 1 +chr10:99423714-99423777:- 1 +chr10:99732246-99732275:+ 1 +chr1:100145183-100145264:+ 1 +chr1:100351338-100351368:- 1 +chr1:108876785-108876812:- 2 +chr1:108876814-108876843:- 1 +chr1:109619694-109619719:- 1 +chr1:112395972-112395999:- 2 +chr11:125124166-125124283:- 1 +chr1:112707236-112707287:+ 1 +chr1:116825902-116826016:- 2 +chr11:1764075-1764105:+ 1 +chr1:1300039-1300072:- 1 +chr11:31811478-31811534:+ 1 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100 +tRNA-Ala-AGC-13-1 374 +tRNA-Ala-AGC-13-2 167 +tRNA-Ala-AGC-14-1 186 +tRNA-Ala-AGC-15-1 103 +tRNA-Ala-AGC-16-1 5 +tRNA-Ala-AGC-17-1 3 +tRNA-Ala-AGC-18-1 137 +tRNA-Ala-AGC-18-2 100 +tRNA-Ala-AGC-19-1 292 +tRNA-Ala-AGC-20-1 2 +tRNA-Ala-AGC-2-1 974 +tRNA-Ala-AGC-21-1 21 +tRNA-Ala-AGC-2-2 1641 +tRNA-Ala-AGC-22-1 179 +tRNA-Ala-AGC-23-1 9 +tRNA-Ala-AGC-3-1 678 +tRNA-Ala-AGC-4-1 4827 +tRNA-Ala-AGC-5-1 1154 +tRNA-Ala-AGC-6-1 2919 +tRNA-Ala-AGC-7-1 1046 +tRNA-Ala-AGC-8-1 652 +tRNA-Ala-AGC-8-2 172 +tRNA-Ala-AGC-9-1 27 +tRNA-Ala-AGC-9-2 26 +tRNA-Ala-AGC-chr6-164 135 +tRNA-Ala-AGC-chr6-166 106 +tRNA-Ala-AGC-chr6-168 154 +tRNA-Ala-AGC-chr6-96 155 +tRNA-Ala-AGC-chr6-97 32 +tRNA-Ala-ATC-chr6-107 2 +tRNA-Ala-CGC-1-1 1565 +tRNA-Ala-CGC-2-1 1344 +tRNA-Ala-CGC-3-1 960 +tRNA-Ala-CGC-4-1 1544 +tRNA-Ala-CGC-5-1 235 +tRNA-Ala-TGC-1-1 1205 +tRNA-Ala-TGC-2-1 1011 +tRNA-Ala-TGC-3-1 1210 +tRNA-Ala-TGC-3-2 1141 +tRNA-Ala-TGC-4-1 2095 +tRNA-Ala-TGC-5-1 914 +tRNA-Ala-TGC-6-1 1247 +tRNA-Ala-TGC-7-1 1176 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+U97 87 +U99 75 +Z17B 602 diff --git a/smRNA-seq/count/HEPG2.srt.dd.q10.oncRNA.cnt b/smRNA-seq/count/HEPG2.srt.dd.q10.oncRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..11d86c89aa6b131830d9e8d3c9b23f52dcffd691 --- /dev/null +++ b/smRNA-seq/count/HEPG2.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,220 @@ +chr10:100373355-100373383:- 1 +chr10:124986417-124986448:+ 1 +chr10:128109065-128109096:- 1 +chr10:22321239-22321269:+ 1 +chr10:59176979-59177010:- 1 +chr10:61901066-61901223:- 1 +chr10:91909034-91909088:+ 1 +chr10:97425871-97425899:- 1 +chr10:99423714-99423777:- 3 +chr10:99732246-99732275:+ 1 +chr11:130069352-130069383:- 1 +chr1:116415681-116415850:- 1 +chr11:1764075-1764105:+ 1 +chr1:119712133-119712165:+ 1 +chr11:32894261-32894290:- 1 +chr11:355961-355990:- 1 +chr1:148402323-148402352:- 1 +chr1:155127664-155127691:- 1 +chr1:15542158-15542189:+ 14 +chr1:15542197-15542228:+ 16 +chr11:57531053-57531082:+ 1 +chr11:64241913-64242102:- 1 +chr11:65421326-65421355:- 1 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0000000000000000000000000000000000000000..17c9798e10580cd7afdfa4fec42370c8325264cb --- /dev/null +++ b/smRNA-seq/count/HS707A.hsa-miR.cnt @@ -0,0 +1,311 @@ +hsa-let-7a-2-3p 6 +hsa-let-7a-3p 33 +hsa-let-7a-5p 975 +hsa-let-7b-3p 53 +hsa-let-7b-5p 657 +hsa-let-7c-3p 1 +hsa-let-7c-5p 72 +hsa-let-7d-3p 14 +hsa-let-7d-5p 64 +hsa-let-7e-3p 3 +hsa-let-7e-5p 218 +hsa-let-7f-1-3p 6 +hsa-let-7f-2-3p 12 +hsa-let-7f-5p 607 +hsa-let-7g-5p 422 +hsa-let-7i-3p 73 +hsa-let-7i-5p 577 +hsa-miR-100-3p 3 +hsa-miR-100-5p 98 +hsa-miR-10400-5p 1 +hsa-miR-106b-3p 5 +hsa-miR-106b-5p 4 +hsa-miR-10b-5p 1 +hsa-miR-1180-5p 1 +hsa-miR-1185-1-3p 1 +hsa-miR-12136 2 +hsa-miR-1228-3p 1 +hsa-miR-1228-5p 3 +hsa-miR-1246 21 +hsa-miR-125a-3p 1 +hsa-miR-125a-5p 259 +hsa-miR-125b-1-3p 6 +hsa-miR-125b-5p 218 +hsa-miR-1260a 3 +hsa-miR-1260b 95 +hsa-miR-126-5p 2 +hsa-miR-1271-5p 1 +hsa-miR-127-3p 2 +hsa-miR-1275 8 +hsa-miR-128-3p 5 +hsa-miR-1290 19 +hsa-miR-129-5p 1 +hsa-miR-1296-5p 1 +hsa-miR-1306-5p 1 +hsa-miR-1307-3p 1 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b/smRNA-seq/count/HS707A.srt.annotated.cnt new file mode 100644 index 0000000000000000000000000000000000000000..a05f7deb634c4b12f191080288d8d15d122f5b1c --- /dev/null +++ b/smRNA-seq/count/HS707A.srt.annotated.cnt @@ -0,0 +1,1092 @@ +14q(0) 484 +14q(I-3) 229 +14q(I-4) 178 +14q(I-5) 344 +14q(I-6) 270 +14q(I-7) 573 +14q(I-8) 583 +14q(I-9) 377 +14q(II-1) 116 +14q(II-10) 1 +14q(II-11) 24 +14q(II-12) 582 +14q(II-13) 38 +14q(II-14) 4 +14q(II-15) 7 +14q(II-16) 1 +14q(II-17) 252 +14q(II-20) 133 +14q(II-21) 34 +14q(II-22) 176 +14q(II-23) 50 +14q(II-24) 1 +14q(II-25) 146 +14q(II-26) 25 +14q(II-28) 72 +14q(II-3) 84 +14q(II-31) 1 +14q(II-5) 1 +14q(II-9) 97 +ACA1 252 +ACA10 111 +ACA11 9 +ACA12 29 +ACA13 290 +ACA14a 2 +ACA14b 160 +ACA15 9 +ACA16 11 +ACA17 291 +ACA18 239 +ACA19 183 +ACA20 385 +ACA21 1038 +ACA22 6 +ACA23 148 +ACA24 156 +ACA25 273 +ACA26 292 +ACA27 74 +ACA28 164 +ACA2a 28 +ACA2b 54 +ACA3 581 +ACA30 40 +ACA31 284 +ACA3-2 601 +ACA32 195 +ACA33 218 +ACA34 20 +ACA35 15 +ACA36 36 +ACA36B 45 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0000000000000000000000000000000000000000..d75b324b72b90c1ba12db2d0848c4e88f3382f62 --- /dev/null +++ b/smRNA-seq/count/HS707A.srt.tRNA.cnt @@ -0,0 +1,491 @@ +nm-tRNA-Tyr-GTA-chr1-142 387 +nm-tRNA-Tyr-GTA-chr14-8 384 +nm-tRNA-Tyr-GTA-chr21-2 339 +nm-tRNA-Tyr-GTA-chr9-4 1 +nm-tRNA-Tyr-NNN-chr2-20 4 +nmt-tRNA-Leu-TAA-4-1 2 +nmt-tRNA-Val-TAC-1-1 1 +tRNA-Ala-AGC-10-1 2 +tRNA-Ala-AGC-1-1 714 +tRNA-Ala-AGC-11-1 211 +tRNA-Ala-AGC-12-1 3 +tRNA-Ala-AGC-12-3 2 +tRNA-Ala-AGC-13-1 57 +tRNA-Ala-AGC-13-2 29 +tRNA-Ala-AGC-14-1 4 +tRNA-Ala-AGC-15-1 76 +tRNA-Ala-AGC-18-1 15 +tRNA-Ala-AGC-18-2 16 +tRNA-Ala-AGC-19-1 33 +tRNA-Ala-AGC-20-1 2 +tRNA-Ala-AGC-2-1 857 +tRNA-Ala-AGC-21-1 3 +tRNA-Ala-AGC-2-2 1162 +tRNA-Ala-AGC-22-1 2 +tRNA-Ala-AGC-3-1 692 +tRNA-Ala-AGC-4-1 4469 +tRNA-Ala-AGC-5-1 917 +tRNA-Ala-AGC-6-1 1931 +tRNA-Ala-AGC-7-1 899 +tRNA-Ala-AGC-8-1 375 +tRNA-Ala-AGC-8-2 170 +tRNA-Ala-AGC-9-1 1 +tRNA-Ala-AGC-9-2 2 +tRNA-Ala-AGC-chr6-164 6 +tRNA-Ala-AGC-chr6-166 2 +tRNA-Ala-AGC-chr6-168 36 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105 +tRNA-Cys-GCA-6-1 9 +tRNA-Cys-GCA-7-1 24 +tRNA-Cys-GCA-8-1 115 +tRNA-Cys-GCA-9-1 5 +tRNA-Cys-GCA-9-2 10 +tRNA-Cys-GCA-9-3 14 +tRNA-Cys-GCA-9-4 19 +tRNA-Cys-GCA-chr11-21 1 +tRNA-Gln-CTG-10-1 1 +tRNA-Gln-CTG-1-1 5296 +tRNA-Gln-CTG-11-1 3 +tRNA-Gln-CTG-1-2 5153 +tRNA-Gln-CTG-1-3 5692 +tRNA-Gln-CTG-1-4 6688 +tRNA-Gln-CTG-1-5 5350 +tRNA-Gln-CTG-2-1 6174 +tRNA-Gln-CTG-3-1 336 +tRNA-Gln-CTG-3-2 333 +tRNA-Gln-CTG-4-1 366 +tRNA-Gln-CTG-4-2 365 +tRNA-Gln-CTG-5-1 789 +tRNA-Gln-CTG-6-1 586 +tRNA-Gln-CTG-7-1 5 +tRNA-Gln-CTG-8-1 17 +tRNA-Gln-CTG-8-2 17 +tRNA-Gln-CTG-9-1 5 +tRNA-Gln-CTG-chr1-130 17 +tRNA-Gln-CTG-chr1-23 12 +tRNA-Gln-TTG-1-1 1771 +tRNA-Gln-TTG-2-1 471 +tRNA-Gln-TTG-3-1 2100 +tRNA-Gln-TTG-3-2 1825 +tRNA-Gln-TTG-3-3 1729 +tRNA-Gln-TTG-4-1 28 +tRNA-Glu-CTC-1-1 2272 +tRNA-Glu-CTC-1-2 2247 +tRNA-Glu-CTC-1-3 2273 +tRNA-Glu-CTC-1-4 2252 +tRNA-Glu-CTC-1-5 2282 +tRNA-Glu-CTC-1-6 2223 +tRNA-Glu-CTC-1-7 1286 +tRNA-Glu-CTC-2-1 2161 +tRNA-Glu-CTC-3-1 9 +tRNA-Glu-GAA-chr1-125 2 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+tRNA-Val-AAC-2-1 622 +tRNA-Val-AAC-3-1 259 +tRNA-Val-AAC-4-1 51 +tRNA-Val-AAC-5-1 32 +tRNA-Val-AAC-6-1 71 +tRNA-Val-CAC-1-1 134 +tRNA-Val-CAC-1-2 135 +tRNA-Val-CAC-1-3 103 +tRNA-Val-CAC-1-4 714 +tRNA-Val-CAC-1-5 331 +tRNA-Val-CAC-1-6 265 +tRNA-Val-CAC-2-1 303 +tRNA-Val-CAC-3-1 1101 +tRNA-Val-CAC-4-1 340 +tRNA-Val-CAC-5-1 175 +tRNA-Val-CAC-6-1 4 +tRNA-Val-CAC-7-1 1 +tRNA-Val-CAC-8-1 3 +tRNA-Val-CAC-chr1-16 83 +tRNA-Val-CAC-chr1-93 184 +tRNA-Val-TAC-1-1 698 +tRNA-Val-TAC-1-2 819 +tRNA-Val-TAC-2-1 2008 +tRNA-Val-TAC-3-1 195 +tRNA-Val-TAC-4-1 51 diff --git a/smRNA-seq/count/MCF7.hsa-miR.cnt b/smRNA-seq/count/MCF7.hsa-miR.cnt new file mode 100644 index 0000000000000000000000000000000000000000..47d1a2665d3ec61358f94dd9e6d4a5bcb75626a4 --- /dev/null +++ b/smRNA-seq/count/MCF7.hsa-miR.cnt @@ -0,0 +1,283 @@ +hsa-let-7a-3p 13 +hsa-let-7a-5p 755 +hsa-let-7b-3p 4 +hsa-let-7b-5p 211 +hsa-let-7c-5p 91 +hsa-let-7d-3p 30 +hsa-let-7d-5p 228 +hsa-let-7e-3p 1 +hsa-let-7e-5p 233 +hsa-let-7f-1-3p 22 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0000000000000000000000000000000000000000..c09e4d56ae7361286a3e102d3267775b94dfd8de --- /dev/null +++ b/smRNA-seq/count/MDA453.srt.annotated.cnt @@ -0,0 +1,1032 @@ +14q(0) 1 +14q(I-8) 1 +14q(II-12) 2 +14q(II-22) 1 +14q(II-25) 1 +ACA1 650 +ACA10 223 +ACA11 20 +ACA12 124 +ACA13 527 +ACA14a 5 +ACA14b 345 +ACA15 60 +ACA16 34 +ACA17 1280 +ACA18 609 +ACA19 362 +ACA20 673 +ACA21 1485 +ACA22 24 +ACA23 148 +ACA24 259 +ACA25 616 +ACA26 923 +ACA27 446 +ACA28 434 +ACA2a 55 +ACA2b 100 +ACA3 508 +ACA30 169 +ACA31 768 +ACA3-2 555 +ACA32 507 +ACA33 505 +ACA34 22 +ACA35 45 +ACA36 217 +ACA36B 104 +ACA37 109 +ACA38 97 +ACA39 457 +ACA4 895 +ACA40 912 +ACA41 192 +ACA42 772 +ACA43 192 +ACA44 332 +ACA45 15 +ACA46 381 +ACA47 12 +ACA48 256 +ACA49 16 +ACA5 178 +ACA50 81 +ACA51 410 +ACA52 64 +ACA53 64 +ACA54 144 +ACA55 278 +ACA56 338 +ACA57 35 +ACA58 354 +ACA59 42 +ACA59B 42 +ACA5b 1 +ACA5c 128 +ACA6 422 +ACA60 172 +ACA61 390 +ACA62 1883 +ACA63 10 +ACA64 69 +ACA65 35 +ACA66 30 +ACA67 19 +ACA67B 37 +ACA68 25 +ACA7 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+tRNA-Val-TAC-1-1 386 +tRNA-Val-TAC-1-2 458 +tRNA-Val-TAC-2-1 1025 +tRNA-Val-TAC-3-1 107 +tRNA-Val-TAC-4-1 3 diff --git a/smRNA-seq/count/PACA2.hsa-miR.cnt b/smRNA-seq/count/PACA2.hsa-miR.cnt new file mode 100644 index 0000000000000000000000000000000000000000..ebe7761a5726bc7760d43990cfd6f06b549b735a --- /dev/null +++ b/smRNA-seq/count/PACA2.hsa-miR.cnt @@ -0,0 +1,252 @@ +hsa-let-7a-3p 19 +hsa-let-7a-5p 768 +hsa-let-7b-3p 16 +hsa-let-7b-5p 221 +hsa-let-7c-5p 5 +hsa-let-7d-3p 15 +hsa-let-7d-5p 154 +hsa-let-7e-3p 2 +hsa-let-7e-5p 102 +hsa-let-7f-1-3p 24 +hsa-let-7f-2-3p 11 +hsa-let-7f-5p 704 +hsa-let-7g-5p 453 +hsa-let-7i-3p 65 +hsa-let-7i-5p 564 +hsa-miR-10400-5p 1 +hsa-miR-106b-3p 5 +hsa-miR-106b-5p 4 +hsa-miR-107 1 +hsa-miR-10a-3p 1 +hsa-miR-10a-5p 4 +hsa-miR-1180-5p 2 +hsa-miR-12135 2 +hsa-miR-12136 11 +hsa-miR-1224-3p 2 +hsa-miR-1226-3p 1 +hsa-miR-1229-3p 1 +hsa-miR-1236-3p 1 +hsa-miR-1246 20 +hsa-miR-125a-3p 1 +hsa-miR-125a-5p 100 +hsa-miR-1260a 1 +hsa-miR-1260b 64 +hsa-miR-126-3p 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25 +tRNA-Phe-GAA-5-1 16 +tRNA-Phe-GAA-6-1 44 +tRNA-Phe-GAA-7-1 1 +tRNA-Phe-GAA-8-1 2 +tRNA-Phe-GAA-9-1 4 +tRNA-Pro-AGG-1-1 372 +tRNA-Pro-AGG-2-1 524 +tRNA-Pro-AGG-2-2 271 +tRNA-Pro-AGG-2-3 468 +tRNA-Pro-AGG-2-4 494 +tRNA-Pro-AGG-2-5 720 +tRNA-Pro-AGG-2-6 530 +tRNA-Pro-AGG-2-7 723 +tRNA-Pro-AGG-2-8 430 +tRNA-Pro-AGG-3-1 1 +tRNA-Pro-CGG-1-1 1319 +tRNA-Pro-CGG-1-2 1085 +tRNA-Pro-CGG-1-3 1659 +tRNA-Pro-CGG-2-1 1879 +tRNA-Pro-TGG-1-1 1055 +tRNA-Pro-TGG-2-1 1697 +tRNA-Pro-TGG-3-1 1533 +tRNA-Pro-TGG-3-2 722 +tRNA-Pro-TGG-3-3 621 +tRNA-Pro-TGG-3-4 4102 +tRNA-Pro-TGG-3-5 3348 +tRNA-SeC-TCA-1-1 3761 +tRNA-SeC-TCA-2-1 62 +tRNA-Ser-ACT-1-1 212 +tRNA-Ser-AGA-1-1 201 +tRNA-Ser-AGA-2-1 232 +tRNA-Ser-AGA-2-2 139 +tRNA-Ser-AGA-2-3 121 +tRNA-Ser-AGA-2-4 145 +tRNA-Ser-AGA-2-5 114 +tRNA-Ser-AGA-2-6 205 +tRNA-Ser-AGA-3-1 136 +tRNA-Ser-AGA-4-1 57 +tRNA-Ser-AGA-5-1 5 +tRNA-Ser-AGA-6-1 1 +tRNA-Ser-CGA-1-1 933 +tRNA-Ser-CGA-2-1 719 +tRNA-Ser-CGA-3-1 1496 +tRNA-Ser-CGA-4-1 486 +tRNA-Ser-GCT-1-1 68 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706 +U14A 353 +U14B 36 +U15A 99 +U15B 576 +U16 342 +U17a 293 +U17b 259 +U18A 115 +U18B 1531 +U18C 847 +U19 470 +U19-2 37 +U20 52 +U21 463 +U22 1814 +U23 1083 +U24 181 +U25 246 +U26 415 +U27 917 +U28 38 +U29 994 +U3 4378 +U30 777 +U31 2080 +U3-2 1590 +U32A 562 +U3-2B 1515 +U3-3 1292 +U33 93 +U3-4 1413 +U34 1889 +U35A 156 +U35B 307 +U36A 112 +U36B 180 +U36C 1132 +U37 185 +U38A 206 +U38B 1181 +U41 4 +U42A 131 +U42B 837 +U43 2153 +U44 1986 +U45A 276 +U45B 12 +U45C 90 +U46 1023 +U47 1160 +U48 408 +U49A 2102 +U49B 648 +U50 32 +U50B 405 +U51 368 +U52 1835 +U53 59 +U54 61 +U55 32 +U56 2193 +U57 43 +U58A 588 +U58B 656 +U58C 120 +U59A 223 +U59B 266 +U60 142 +U61 104 +U62A 1120 +U62B 1126 +U63 1206 +U64 1319 +U65 1451 +U66 414 +U67 436 +U68 900 +U69 839 +U70 675 +U70B 1 +U71a 272 +U71b 684 +U71c 179 +U71d 774 +U72 508 +U73a 148 +U73b 10 +U74 1718 +U75 1878 +U76 831 +U77 2260 +U78 476 +U79 2218 +U8 3746 +U80 578 +U81 549 +U82 1785 +U83 682 +U83A 903 +U83B 1480 +U84 973 +U85 44 +U86 45 +U87 28 +U88 13 +U89 10 +U90 2 +U91 1 +U92 64 +U93 14 +U94 84 +U95 1042 +U96a 572 +U97 70 +U99 76 +Z17B 665 diff --git a/smRNA-seq/count/PACA2.srt.dd.q10.oncRNA.cnt b/smRNA-seq/count/PACA2.srt.dd.q10.oncRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..0d1b0dd62ab0f4d48cbd759e8424ffe6f56155a7 --- /dev/null +++ b/smRNA-seq/count/PACA2.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,400 @@ +chr10:102450480-102450516:- 1 +chr10:102642093-102642123:- 1 +chr10:113045362-113045392:+ 1 +chr10:128115651-128115681:- 1 +chr10:13348424-13348453:+ 2 +chr10:134966-134992:+ 1 +chr10:15169088-15169116:+ 1 +chr10:16986124-16986267:- 1 +chr10:3784012-3784065:+ 1 +chr10:43647920-43647969:+ 1 +chr10:68328667-68328760:+ 1 +chr10:68407561-68407604:+ 1 +chr10:78973622-78973649:- 1 +chr10:91798206-91798233:- 2 +chr10:97497753-97497787:- 1 +chr10:97689864-97690057:+ 1 +chr10:99659225-99659254:- 1 +chr1:100896172-100896205:+ 2 +chr1:108897479-108897651:+ 1 +chr1:109100593-109100623:- 1 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448 +tRNA-Val-TAC-1-2 728 +tRNA-Val-TAC-2-1 1529 +tRNA-Val-TAC-3-1 406 +tRNA-Val-TAC-4-1 8 diff --git a/smRNA-seq/count/PANC1.hsa-miR.cnt b/smRNA-seq/count/PANC1.hsa-miR.cnt new file mode 100644 index 0000000000000000000000000000000000000000..f01b9908302bae2682cd3e3e54ae2bea9f20a291 --- /dev/null +++ b/smRNA-seq/count/PANC1.hsa-miR.cnt @@ -0,0 +1,307 @@ +hsa-let-7a-2-3p 1 +hsa-let-7a-3p 27 +hsa-let-7a-5p 838 +hsa-let-7b-3p 23 +hsa-let-7b-5p 361 +hsa-let-7c-5p 6 +hsa-let-7d-3p 6 +hsa-let-7d-5p 49 +hsa-let-7e-3p 1 +hsa-let-7e-5p 181 +hsa-let-7f-1-3p 6 +hsa-let-7f-2-3p 13 +hsa-let-7f-5p 528 +hsa-let-7g-5p 261 +hsa-let-7i-3p 22 +hsa-let-7i-5p 121 +hsa-miR-100-5p 7 +hsa-miR-106b-3p 3 +hsa-miR-106b-5p 3 +hsa-miR-107 1 +hsa-miR-10a-3p 5 +hsa-miR-10a-5p 58 +hsa-miR-10b-3p 1 +hsa-miR-10b-5p 3 +hsa-miR-1180-5p 2 +hsa-miR-1185-1-3p 1 +hsa-miR-1185-2-3p 1 +hsa-miR-12135 1 +hsa-miR-12136 6 +hsa-miR-1226-3p 1 +hsa-miR-1246 10 +hsa-miR-125a-3p 1 +hsa-miR-125a-5p 185 +hsa-miR-125b-1-3p 1 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35 diff --git a/smRNA-seq/count/PANC1.srt.annotated.cnt b/smRNA-seq/count/PANC1.srt.annotated.cnt new file mode 100644 index 0000000000000000000000000000000000000000..c34c8962c3560e0a88d0f882df9254eb1bc32f50 --- /dev/null +++ b/smRNA-seq/count/PANC1.srt.annotated.cnt @@ -0,0 +1,1090 @@ +14q(0) 249 +14q(I-3) 86 +14q(I-4) 73 +14q(I-5) 184 +14q(I-6) 153 +14q(I-7) 253 +14q(I-8) 190 +14q(I-9) 205 +14q(II-1) 21 +14q(II-11) 7 +14q(II-12) 213 +14q(II-13) 24 +14q(II-14) 3 +14q(II-15) 1 +14q(II-17) 172 +14q(II-20) 58 +14q(II-21) 19 +14q(II-22) 104 +14q(II-23) 24 +14q(II-24) 3 +14q(II-25) 55 +14q(II-26) 23 +14q(II-28) 22 +14q(II-3) 33 +14q(II-9) 21 +ACA1 610 +ACA10 211 +ACA11 12 +ACA12 41 +ACA13 565 +ACA14a 16 +ACA14b 313 +ACA15 65 +ACA16 26 +ACA17 499 +ACA18 619 +ACA19 570 +ACA20 856 +ACA21 1128 +ACA22 19 +ACA23 464 +ACA24 205 +ACA25 706 +ACA26 847 +ACA27 228 +ACA28 249 +ACA2a 50 +ACA2b 74 +ACA3 1406 +ACA30 99 +ACA31 375 +ACA3-2 1405 +ACA32 552 +ACA33 567 +ACA34 23 +ACA35 50 +ACA36 160 +ACA36B 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106 +U61 221 +U62A 473 +U62B 478 +U63 665 +U64 1144 +U65 699 +U66 226 +U67 249 +U68 688 +U69 629 +U70 607 +U70B 3 +U71a 152 +U71b 483 +U71c 88 +U71d 550 +U72 877 +U73a 154 +U73b 6 +U74 852 +U75 1056 +U76 796 +U77 1309 +U78 279 +U79 1521 +U8 957 +U80 301 +U81 492 +U82 1148 +U83 563 +U83A 577 +U83B 793 +U84 744 +U85 14 +U86 6 +U87 22 +U88 6 +U89 4 +U90 2 +U92 29 +U93 7 +U94 48 +U95 507 +U96a 369 +U97 119 +U99 102 +Z17B 589 diff --git a/smRNA-seq/count/PANC1.srt.dd.q10.oncRNA.cnt b/smRNA-seq/count/PANC1.srt.dd.q10.oncRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..4f7a8d9bae5a2dac8a6a6252f3f9789f3df475f4 --- /dev/null +++ b/smRNA-seq/count/PANC1.srt.dd.q10.oncRNA.cnt @@ -0,0 +1,162 @@ +chr10:102450480-102450516:- 1 +chr10:112950886-112950915:+ 1 +chr10:119061323-119061355:- 1 +chr10:43387469-43387499:- 1 +chr10:45001299-45001331:- 1 +chr10:68471686-68471716:- 1 +chr10:68600645-68600753:- 1 +chr10:69597459-69597517:+ 1 +chr10:73915228-73915260:+ 1 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2 +chr7:64837467-64837498:+ 1 +chr7:64902669-64902793:- 1 +chr8:119855972-119855997:+ 1 +chr8:141414461-141414603:- 1 +chr8:144138633-144138667:+ 1 +chr8:91070320-91070348:+ 1 +chr9:122886503-122886539:+ 5 +chr9:34610606-34610662:- 1 +chr9:36925084-36925146:+ 1 +chr9:92711622-92711649:- 1 +chrX:108736297-108736330:- 1 +chrX:12970744-12970926:+ 1 +chrX:153862891-153862949:- 1 +chrX:154442915-154442946:+ 1 +chrX:154478827-154478854:- 1 diff --git a/smRNA-seq/count/PANC1.srt.tRNA.cnt b/smRNA-seq/count/PANC1.srt.tRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..a4ce03c32141b54e3e73aecb82d6544908a0451e --- /dev/null +++ b/smRNA-seq/count/PANC1.srt.tRNA.cnt @@ -0,0 +1,497 @@ +nm-tRNA-SerTGA-AGA-chr11-7 1 +nm-tRNA-Tyr-GTA-chr1-142 239 +nm-tRNA-Tyr-GTA-chr14-8 242 +nm-tRNA-Tyr-GTA-chr21-2 236 +nm-tRNA-Tyr-NNN-chr2-20 1 +nmt-tRNA-Gln-TTG-9-1 1 +nmt-tRNA-Leu-TAA-4-1 1 +nmt-tRNA-Val-TAC-1-1 8 +tRNA-Ala-AGC-10-1 601 +tRNA-Ala-AGC-1-1 1016 +tRNA-Ala-AGC-11-1 448 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+tRNA-Tyr-GTA-5-4 333 +tRNA-Tyr-GTA-5-5 90 +tRNA-Tyr-GTA-6-1 30 +tRNA-Tyr-GTA-7-1 39 +tRNA-Tyr-GTA-8-1 67 +tRNA-Und-NNN-3-1 5 +tRNA-Val-AAC-1-1 150 +tRNA-Val-AAC-1-2 137 +tRNA-Val-AAC-1-3 120 +tRNA-Val-AAC-1-4 120 +tRNA-Val-AAC-1-5 101 +tRNA-Val-AAC-2-1 385 +tRNA-Val-AAC-3-1 256 +tRNA-Val-AAC-4-1 67 +tRNA-Val-AAC-5-1 66 +tRNA-Val-AAC-6-1 232 +tRNA-Val-CAC-1-1 166 +tRNA-Val-CAC-11-2 23 +tRNA-Val-CAC-1-2 248 +tRNA-Val-CAC-1-3 165 +tRNA-Val-CAC-1-4 595 +tRNA-Val-CAC-1-5 215 +tRNA-Val-CAC-1-6 274 +tRNA-Val-CAC-2-1 388 +tRNA-Val-CAC-3-1 502 +tRNA-Val-CAC-4-1 178 +tRNA-Val-CAC-5-1 205 +tRNA-Val-CAC-6-1 112 +tRNA-Val-CAC-8-1 9 +tRNA-Val-CAC-9-1 127 +tRNA-Val-CAC-chr1-134 1 +tRNA-Val-CAC-chr1-136 23 +tRNA-Val-CAC-chr1-16 248 +tRNA-Val-CAC-chr1-93 171 +tRNA-Val-TAC-1-1 796 +tRNA-Val-TAC-1-2 876 +tRNA-Val-TAC-2-1 2125 +tRNA-Val-TAC-3-1 643 +tRNA-Val-TAC-4-1 255 diff --git a/smRNA-seq/count/PC3.srt.annotated.cnt b/smRNA-seq/count/PC3.srt.annotated.cnt new file mode 100644 index 0000000000000000000000000000000000000000..351dffc94e48df0ba8e92b3766c01015b7e8e7d7 --- /dev/null +++ b/smRNA-seq/count/PC3.srt.annotated.cnt @@ -0,0 +1,1030 @@ +14q(0) 2 +14q(I-3) 1 +14q(I-4) 1 +14q(I-5) 5 +14q(I-6) 2 +14q(I-7) 5 +14q(I-8) 5 +14q(I-9) 2 +14q(II-12) 6 +14q(II-17) 4 +14q(II-23) 2 +14q(II-25) 4 +14q(II-3) 1 +ACA1 353 +ACA10 130 +ACA11 32 +ACA12 120 +ACA13 581 +ACA14a 21 +ACA14b 123 +ACA15 61 +ACA16 21 +ACA17 411 +ACA18 367 +ACA19 307 +ACA20 701 +ACA21 1117 +ACA22 15 +ACA23 347 +ACA24 229 +ACA25 549 +ACA26 754 +ACA27 204 +ACA28 318 +ACA2a 63 +ACA2b 68 +ACA3 951 +ACA30 74 +ACA31 450 +ACA3-2 1037 +ACA32 296 +ACA33 415 +ACA34 34 +ACA35 36 +ACA36 97 +ACA36B 63 +ACA37 144 +ACA38 38 +ACA39 220 +ACA4 1072 +ACA40 757 +ACA41 192 +ACA42 601 +ACA43 33 +ACA44 201 +ACA45 125 +ACA46 249 +ACA47 40 +ACA48 363 +ACA49 54 +ACA5 178 +ACA50 53 +ACA51 624 +ACA52 66 +ACA53 104 +ACA54 126 +ACA55 150 +ACA56 142 +ACA57 29 +ACA58 305 +ACA59 21 +ACA59B 18 +ACA5c 111 +ACA6 575 +ACA60 67 +ACA61 258 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b/smRNA-seq/count/PC3.srt.tRNA.cnt new file mode 100644 index 0000000000000000000000000000000000000000..06dee2e3f4ad0e9a94a30ccfc2b362732a705235 --- /dev/null +++ b/smRNA-seq/count/PC3.srt.tRNA.cnt @@ -0,0 +1,484 @@ +nm-tRNA-Tyr-GTA-chr1-142 295 +nm-tRNA-Tyr-GTA-chr14-8 337 +nm-tRNA-Tyr-GTA-chr21-2 305 +nm-tRNA-Tyr-NNN-chr2-20 1 +nmt-tRNA-Leu-TAA-1-1 1 +nmt-tRNA-Leu-TAA-4-1 1 +nmt-tRNA-Val-TAC-1-1 6 +tRNA-Ala-AGC-10-1 30 +tRNA-Ala-AGC-1-1 559 +tRNA-Ala-AGC-11-1 261 +tRNA-Ala-AGC-12-1 22 +tRNA-Ala-AGC-12-2 15 +tRNA-Ala-AGC-12-3 15 +tRNA-Ala-AGC-13-1 69 +tRNA-Ala-AGC-13-2 30 +tRNA-Ala-AGC-14-1 30 +tRNA-Ala-AGC-15-1 10 +tRNA-Ala-AGC-16-1 3 +tRNA-Ala-AGC-18-2 1 +tRNA-Ala-AGC-19-1 1 +tRNA-Ala-AGC-20-1 1 +tRNA-Ala-AGC-2-1 920 +tRNA-Ala-AGC-21-1 1 +tRNA-Ala-AGC-2-2 1219 +tRNA-Ala-AGC-22-1 1 +tRNA-Ala-AGC-3-1 658 +tRNA-Ala-AGC-4-1 3857 +tRNA-Ala-AGC-5-1 644 +tRNA-Ala-AGC-6-1 1405 +tRNA-Ala-AGC-7-1 1086 +tRNA-Ala-AGC-8-1 569 +tRNA-Ala-AGC-8-2 307 +tRNA-Ala-AGC-chr6-164 13 +tRNA-Ala-AGC-chr6-166 20 +tRNA-Ala-AGC-chr6-168 22 +tRNA-Ala-AGC-chr6-96 26 +tRNA-Ala-ATC-chr6-107 1 +tRNA-Ala-CGC-1-1 1344 +tRNA-Ala-CGC-2-1 1262 +tRNA-Ala-CGC-3-1 1150 +tRNA-Ala-CGC-4-1 1516 +tRNA-Ala-CGC-5-1 208 +tRNA-Ala-TGC-1-1 827 +tRNA-Ala-TGC-2-1 745 +tRNA-Ala-TGC-3-1 1242 +tRNA-Ala-TGC-3-2 1335 +tRNA-Ala-TGC-4-1 2837 +tRNA-Ala-TGC-5-1 595 +tRNA-Ala-TGC-6-1 511 +tRNA-Ala-TGC-7-1 707 +tRNA-Ala-TGC-8-1 1 +tRNA-Arg-ACG-1-1 140 +tRNA-Arg-ACG-1-2 175 +tRNA-Arg-ACG-1-3 125 +tRNA-Arg-ACG-2-1 208 +tRNA-Arg-ACG-2-2 73 +tRNA-Arg-ACG-2-3 160 +tRNA-Arg-ACG-2-4 200 +tRNA-Arg-CCG-1-1 813 +tRNA-Arg-CCG-1-2 1370 +tRNA-Arg-CCG-1-3 775 +tRNA-Arg-CCG-2-1 7958 +tRNA-Arg-CCT-1-1 3449 +tRNA-Arg-CCT-2-1 3645 +tRNA-Arg-CCT-3-1 1119 +tRNA-Arg-CCT-4-1 4020 +tRNA-Arg-CCT-5-1 14 +tRNA-Arg-TCG-1-1 488 +tRNA-Arg-TCG-2-1 151 +tRNA-Arg-TCG-3-1 1169 +tRNA-Arg-TCG-4-1 65 +tRNA-Arg-TCG-5-1 230 +tRNA-Arg-TCT-1-1 231 +tRNA-Arg-TCT-2-1 315 +tRNA-Arg-TCT-3-1 78 +tRNA-Arg-TCT-3-2 281 +tRNA-Arg-TCT-4-1 25 +tRNA-Arg-TCT-5-1 22 +tRNA-Asn-ATT-1-1 14 +tRNA-Asn-ATT-1-2 12 +tRNA-Asn-GTT-10-1 5 +tRNA-Asn-GTT-1-1 558 +tRNA-Asn-GTT-12-1 1 +tRNA-Asn-GTT-15-1 1 +tRNA-Asn-GTT-17-1 52 +tRNA-Asn-GTT-20-1 1 +tRNA-Asn-GTT-2-1 94 +tRNA-Asn-GTT-2-2 98 +tRNA-Asn-GTT-2-3 165 +tRNA-Asn-GTT-2-4 107 +tRNA-Asn-GTT-2-5 283 +tRNA-Asn-GTT-2-6 134 +tRNA-Asn-GTT-3-1 344 +tRNA-Asn-GTT-4-1 4 +tRNA-Asn-GTT-6-1 4 +tRNA-Asn-GTT-7-1 42 +tRNA-Asn-GTT-8-1 4 +tRNA-Asn-GTT-chr1-110 115 +tRNA-Asn-GTT-chr1-140 8 +tRNA-Asn-GTT-chr1-21 1114 +tRNA-Asn-GTT-chr1-29 347 +tRNA-Asn-GTT-chr1-99 9 +tRNA-Asp-GTC-1-1 1484 +tRNA-Asp-GTC-2-1 713 +tRNA-Asp-GTC-2-10 795 +tRNA-Asp-GTC-2-11 1255 +tRNA-Asp-GTC-2-2 734 +tRNA-Asp-GTC-2-3 758 +tRNA-Asp-GTC-2-4 761 +tRNA-Asp-GTC-2-5 739 +tRNA-Asp-GTC-2-6 1860 +tRNA-Asp-GTC-2-7 1988 +tRNA-Asp-GTC-2-8 2682 +tRNA-Asp-GTC-2-9 849 +tRNA-Asp-GTC-3-1 793 +tRNA-Asp-GTC-4-1 4 +tRNA-Asp-GTC-5-1 655 +tRNA-Cys-GCA-10-1 20 +tRNA-Cys-GCA-1-1 41 +tRNA-Cys-GCA-11-1 1 +tRNA-Cys-GCA-12-1 4 +tRNA-Cys-GCA-13-1 36 +tRNA-Cys-GCA-14-1 153 +tRNA-Cys-GCA-15-1 13 +tRNA-Cys-GCA-16-1 3 +tRNA-Cys-GCA-17-1 25 +tRNA-Cys-GCA-18-1 2 +tRNA-Cys-GCA-19-1 7 +tRNA-Cys-GCA-20-1 4 +tRNA-Cys-GCA-2-1 65 +tRNA-Cys-GCA-21-1 4 +tRNA-Cys-GCA-2-2 111 +tRNA-Cys-GCA-22-1 1 +tRNA-Cys-GCA-2-3 84 +tRNA-Cys-GCA-23-1 3 +tRNA-Cys-GCA-2-4 162 +tRNA-Cys-GCA-25-1 1 +tRNA-Cys-GCA-3-1 10 +tRNA-Cys-GCA-4-1 84 +tRNA-Cys-GCA-5-1 42 +tRNA-Cys-GCA-6-1 33 +tRNA-Cys-GCA-7-1 24 +tRNA-Cys-GCA-8-1 140 +tRNA-Cys-GCA-9-1 18 +tRNA-Cys-GCA-9-2 19 +tRNA-Cys-GCA-9-3 18 +tRNA-Cys-GCA-9-4 15 +tRNA-Gln-CTG-10-1 1 +tRNA-Gln-CTG-1-1 4358 +tRNA-Gln-CTG-11-1 1 +tRNA-Gln-CTG-1-2 4203 +tRNA-Gln-CTG-12-1 1 +tRNA-Gln-CTG-1-3 4593 +tRNA-Gln-CTG-1-4 5384 +tRNA-Gln-CTG-1-5 4317 +tRNA-Gln-CTG-2-1 5263 +tRNA-Gln-CTG-3-1 156 +tRNA-Gln-CTG-3-2 147 +tRNA-Gln-CTG-4-1 312 +tRNA-Gln-CTG-4-2 289 +tRNA-Gln-CTG-5-1 697 +tRNA-Gln-CTG-6-1 1166 +tRNA-Gln-CTG-7-1 7 +tRNA-Gln-CTG-8-1 23 +tRNA-Gln-CTG-8-2 16 +tRNA-Gln-CTG-9-1 13 +tRNA-Gln-CTG-chr1-130 22 +tRNA-Gln-CTG-chr1-23 13 +tRNA-Gln-TTG-1-1 2370 +tRNA-Gln-TTG-2-1 92 +tRNA-Gln-TTG-3-1 1905 +tRNA-Gln-TTG-3-2 1760 +tRNA-Gln-TTG-3-3 1744 +tRNA-Gln-TTG-4-1 22 +tRNA-Glu-CTC-1-1 2738 +tRNA-Glu-CTC-1-2 2648 +tRNA-Glu-CTC-1-3 2713 +tRNA-Glu-CTC-1-4 2647 +tRNA-Glu-CTC-1-5 2779 +tRNA-Glu-CTC-1-6 2675 +tRNA-Glu-CTC-1-7 1629 +tRNA-Glu-CTC-2-1 2624 +tRNA-Glu-CTC-3-1 9 +tRNA-Glu-GAA-chr1-125 4 +tRNA-Glu-GAA-chr1-18 13 +tRNA-Glu-TTC-1-1 1266 +tRNA-Glu-TTC-1-2 1168 +tRNA-Glu-TTC-2-1 2282 +tRNA-Glu-TTC-2-2 1203 +tRNA-Glu-TTC-3-1 133 +tRNA-Glu-TTC-4-2 190 +tRNA-Glu-TTC-5-1 95 +tRNA-Glu-TTC-6-1 2 +tRNA-Glu-TTC-9-1 2 +tRNA-Glu-TTC-chr1-138 176 +tRNA-Gly-CAC-chr1-17 5 +tRNA-Gly-CAC-chr1-94 6 +tRNA-Gly-CCC-1-2 1064 +tRNA-Gly-CCC-2-1 867 +tRNA-Gly-CCC-2-2 1405 +tRNA-Gly-CCC-6-1 232 +tRNA-Gly-CCC-7-1 129 +tRNA-Gly-CCC-chr1-135 290 +tRNA-Gly-CCC-chr1-137 1113 +tRNA-Gly-CCC-chr1-2 17 +tRNA-Gly-GCC-1-1 1516 +tRNA-Gly-GCC-1-2 1607 +tRNA-Gly-GCC-1-3 1495 +tRNA-Gly-GCC-1-4 1480 +tRNA-Gly-GCC-1-5 1485 +tRNA-Gly-GCC-2-1 2069 +tRNA-Gly-GCC-2-2 1319 +tRNA-Gly-GCC-2-3 1677 +tRNA-Gly-GCC-2-4 1470 +tRNA-Gly-GCC-2-5 1862 +tRNA-Gly-GCC-2-6 2288 +tRNA-Gly-GCC-3-1 853 +tRNA-Gly-GCC-4-1 1 +tRNA-Gly-GCC-5-1 11 +tRNA-Gly-TCC-1-1 2627 +tRNA-Gly-TCC-2-1 1666 +tRNA-Gly-TCC-2-2 1265 +tRNA-Gly-TCC-2-3 1313 +tRNA-Gly-TCC-2-4 1293 +tRNA-Gly-TCC-2-5 1345 +tRNA-Gly-TCC-2-6 2176 +tRNA-Gly-TCC-3-1 3695 +tRNA-Gly-TCC-4-1 11 +tRNA-His-GTG-1-1 1565 +tRNA-His-GTG-1-2 1634 +tRNA-His-GTG-1-3 1553 +tRNA-His-GTG-1-4 2171 +tRNA-His-GTG-1-5 2645 +tRNA-His-GTG-1-6 2477 +tRNA-His-GTG-1-7 2335 +tRNA-His-GTG-1-8 2226 +tRNA-His-GTG-1-9 1619 +tRNA-His-GTG-2-1 7 +tRNA-Ile-AAT-1-1 4 +tRNA-Ile-AAT-2-1 30 +tRNA-Ile-AAT-3-1 28 +tRNA-Ile-AAT-4-1 22 +tRNA-Ile-AAT-5-1 202 +tRNA-Ile-AAT-5-2 59 +tRNA-Ile-AAT-5-3 137 +tRNA-Ile-AAT-5-4 77 +tRNA-Ile-AAT-5-5 67 +tRNA-Ile-AAT-6-1 6 +tRNA-Ile-AAT-7-1 6 +tRNA-Ile-AAT-7-2 10 +tRNA-Ile-AAT-8-1 333 +tRNA-Ile-GAT-1-1 1 +tRNA-Ile-TAT-1-1 548 +tRNA-Ile-TAT-2-1 159 +tRNA-Ile-TAT-2-2 47 +tRNA-Ile-TAT-2-3 46 +tRNA-Ile-TAT-3-1 7 +tRNA-iMet-CAT-1-1 1010 +tRNA-iMet-CAT-1-2 376 +tRNA-iMet-CAT-1-3 311 +tRNA-iMet-CAT-1-4 266 +tRNA-iMet-CAT-1-5 191 +tRNA-iMet-CAT-1-6 341 +tRNA-iMet-CAT-1-7 191 +tRNA-iMet-CAT-1-8 160 +tRNA-iMet-CAT-2-1 279 +tRNA-Leu-AAG-1-1 824 +tRNA-Leu-AAG-1-2 221 +tRNA-Leu-AAG-1-3 870 +tRNA-Leu-AAG-2-1 267 +tRNA-Leu-AAG-2-2 1243 +tRNA-Leu-AAG-2-3 255 +tRNA-Leu-AAG-2-4 353 +tRNA-Leu-AAG-3-1 164 +tRNA-Leu-AAG-4-1 16 +tRNA-Leu-AAG-6-1 1 +tRNA-Leu-CAA-1-1 183 +tRNA-Leu-CAA-1-2 367 +tRNA-Leu-CAA-2-1 64 +tRNA-Leu-CAA-3-1 47 +tRNA-Leu-CAA-4-1 548 +tRNA-Leu-CAA-6-1 1 +tRNA-Leu-CAG-1-1 52 +tRNA-Leu-CAG-1-2 70 +tRNA-Leu-CAG-1-3 58 +tRNA-Leu-CAG-1-4 48 +tRNA-Leu-CAG-1-5 61 +tRNA-Leu-CAG-1-6 627 +tRNA-Leu-CAG-1-7 71 +tRNA-Leu-CAG-2-1 82 +tRNA-Leu-CAG-2-2 574 +tRNA-Leu-CAG-chr9-7 16 +tRNA-Leu-TAA-1-1 108 +tRNA-Leu-TAA-2-1 8 +tRNA-Leu-TAA-3-1 45 +tRNA-Leu-TAA-4-1 7 +tRNA-Leu-TAA-5-1 1 +tRNA-Leu-TAG-1-1 995 +tRNA-Leu-TAG-2-1 440 +tRNA-Leu-TAG-3-1 1199 +tRNA-Lys-CTT-10-1 5 +tRNA-Lys-CTT-1-1 3820 +tRNA-Lys-CTT-11-1 542 +tRNA-Lys-CTT-1-2 3511 +tRNA-Lys-CTT-12-1 1 +tRNA-Lys-CTT-14-1 3 +tRNA-Lys-CTT-2-1 1995 +tRNA-Lys-CTT-2-2 2042 +tRNA-Lys-CTT-2-3 2401 +tRNA-Lys-CTT-2-4 2012 +tRNA-Lys-CTT-2-5 1863 +tRNA-Lys-CTT-3-1 157 +tRNA-Lys-CTT-4-1 230 +tRNA-Lys-CTT-5-1 23 +tRNA-Lys-CTT-6-1 108 +tRNA-Lys-CTT-7-1 11 +tRNA-Lys-CTT-9-1 7 +tRNA-Lys-CTT-chr15-5 130 +tRNA-Lys-CTT-chr16-1 1 +tRNA-Lys-CTT-chr7-30 29 +tRNA-Lys-TTT-1-1 146 +tRNA-Lys-TTT-11-1 3 +tRNA-Lys-TTT-12-1 4 +tRNA-Lys-TTT-13-1 12 +tRNA-Lys-TTT-14-1 170 +tRNA-Lys-TTT-15-1 1 +tRNA-Lys-TTT-2-1 148 +tRNA-Lys-TTT-3-1 1356 +tRNA-Lys-TTT-3-2 931 +tRNA-Lys-TTT-3-3 703 +tRNA-Lys-TTT-3-4 780 +tRNA-Lys-TTT-3-5 661 +tRNA-Lys-TTT-4-1 452 +tRNA-Lys-TTT-5-1 405 +tRNA-Lys-TTT-6-1 235 +tRNA-Lys-TTT-7-1 302 +tRNA-Lys-TTT-8-1 2 +tRNA-Lys-TTT-9-1 19 +tRNA-Lys-TTT-chr3-2 1 +tRNA-Met-CAT-1-1 2294 +tRNA-Met-CAT-2-1 6 +tRNA-Met-CAT-3-1 153 +tRNA-Met-CAT-3-2 1303 +tRNA-Met-CAT-4-1 29 +tRNA-Met-CAT-4-2 11 +tRNA-Met-CAT-4-3 22 +tRNA-Met-CAT-6-1 185 +tRNA-Met-CAT-chr6-167 1 +tRNA-Phe-GAA-10-1 3 +tRNA-Phe-GAA-1-1 61 +tRNA-Phe-GAA-1-2 67 +tRNA-Phe-GAA-1-3 48 +tRNA-Phe-GAA-1-4 157 +tRNA-Phe-GAA-1-5 88 +tRNA-Phe-GAA-1-6 45 +tRNA-Phe-GAA-2-1 82 +tRNA-Phe-GAA-3-1 66 +tRNA-Phe-GAA-4-1 12 +tRNA-Phe-GAA-5-1 13 +tRNA-Phe-GAA-6-1 3 +tRNA-Phe-GAA-8-1 1 +tRNA-Phe-GAA-9-1 10 +tRNA-Pro-AGG-1-1 235 +tRNA-Pro-AGG-2-1 387 +tRNA-Pro-AGG-2-2 195 +tRNA-Pro-AGG-2-3 193 +tRNA-Pro-AGG-2-4 388 +tRNA-Pro-AGG-2-5 427 +tRNA-Pro-AGG-2-6 413 +tRNA-Pro-AGG-2-7 413 +tRNA-Pro-AGG-2-8 191 +tRNA-Pro-CGG-1-1 962 +tRNA-Pro-CGG-1-2 866 +tRNA-Pro-CGG-1-3 1403 +tRNA-Pro-CGG-2-1 1252 +tRNA-Pro-TGG-1-1 573 +tRNA-Pro-TGG-2-1 2144 +tRNA-Pro-TGG-3-1 1236 +tRNA-Pro-TGG-3-2 458 +tRNA-Pro-TGG-3-3 417 +tRNA-Pro-TGG-3-4 3593 +tRNA-Pro-TGG-3-5 2793 +tRNA-SeC-TCA-1-1 1956 +tRNA-SeC-TCA-2-1 25 +tRNA-Ser-ACT-1-1 69 +tRNA-Ser-AGA-1-1 109 +tRNA-Ser-AGA-2-1 133 +tRNA-Ser-AGA-2-2 68 +tRNA-Ser-AGA-2-3 81 +tRNA-Ser-AGA-2-4 69 +tRNA-Ser-AGA-2-5 102 +tRNA-Ser-AGA-2-6 115 +tRNA-Ser-AGA-3-1 59 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20 +tRNA-Tyr-GTA-1-1 40 +tRNA-Tyr-GTA-2-1 494 +tRNA-Tyr-GTA-3-1 13 +tRNA-Tyr-GTA-4-1 7 +tRNA-Tyr-GTA-5-1 290 +tRNA-Tyr-GTA-5-2 13 +tRNA-Tyr-GTA-5-3 26 +tRNA-Tyr-GTA-5-4 311 +tRNA-Tyr-GTA-5-5 267 +tRNA-Tyr-GTA-6-1 10 +tRNA-Tyr-GTA-7-1 39 +tRNA-Tyr-GTA-8-1 22 +tRNA-Val-AAC-1-1 175 +tRNA-Val-AAC-1-2 115 +tRNA-Val-AAC-1-3 102 +tRNA-Val-AAC-1-4 132 +tRNA-Val-AAC-1-5 116 +tRNA-Val-AAC-2-1 550 +tRNA-Val-AAC-3-1 319 +tRNA-Val-AAC-4-1 40 +tRNA-Val-AAC-5-1 9 +tRNA-Val-AAC-6-1 235 +tRNA-Val-CAC-1-1 158 +tRNA-Val-CAC-11-2 4 +tRNA-Val-CAC-1-2 259 +tRNA-Val-CAC-1-3 173 +tRNA-Val-CAC-1-4 690 +tRNA-Val-CAC-1-5 225 +tRNA-Val-CAC-1-6 322 +tRNA-Val-CAC-2-1 357 +tRNA-Val-CAC-3-1 979 +tRNA-Val-CAC-4-1 280 +tRNA-Val-CAC-5-1 203 +tRNA-Val-CAC-6-1 2 +tRNA-Val-CAC-8-1 7 +tRNA-Val-CAC-9-1 4 +tRNA-Val-CAC-chr1-136 3 +tRNA-Val-CAC-chr1-16 99 +tRNA-Val-CAC-chr1-93 189 +tRNA-Val-TAC-1-1 864 +tRNA-Val-TAC-1-2 976 +tRNA-Val-TAC-2-1 1729 +tRNA-Val-TAC-3-1 199 +tRNA-Val-TAC-4-1 19 diff --git a/smRNA-seq/count/SW480u.hsa-miR.cnt b/smRNA-seq/count/SW480u.hsa-miR.cnt new file mode 100644 index 0000000000000000000000000000000000000000..2469e834d260d330f49f0988c3a45e1608dd350a --- /dev/null +++ b/smRNA-seq/count/SW480u.hsa-miR.cnt @@ -0,0 +1,257 @@ +hsa-let-7a-3p 29 +hsa-let-7a-5p 789 +hsa-let-7b-3p 27 +hsa-let-7b-5p 498 +hsa-let-7c-5p 2 +hsa-let-7d-3p 30 +hsa-let-7d-5p 117 +hsa-let-7e-3p 3 +hsa-let-7e-5p 151 +hsa-let-7f-1-3p 44 +hsa-let-7f-2-3p 18 +hsa-let-7f-5p 740 +hsa-let-7g-3p 2 +hsa-let-7g-5p 479 +hsa-let-7i-3p 19 +hsa-let-7i-5p 131 +hsa-miR-10400-5p 1 +hsa-miR-106b-3p 12 +hsa-miR-106b-5p 10 +hsa-miR-10a-3p 9 +hsa-miR-10a-5p 33 +hsa-miR-10b-5p 1 +hsa-miR-1180-5p 4 +hsa-miR-12136 4 +hsa-miR-1226-3p 1 +hsa-miR-1246 58 +hsa-miR-125a-3p 2 +hsa-miR-125a-5p 209 +hsa-miR-125b-1-3p 1 +hsa-miR-1260a 2 +hsa-miR-1260b 6 +hsa-miR-126-3p 5 +hsa-miR-126-5p 12 +hsa-miR-1275 25 +hsa-miR-128-3p 12 +hsa-miR-1285-5p 2 +hsa-miR-1290 35 +hsa-miR-1292-5p 1 +hsa-miR-1296-5p 2 +hsa-miR-1304-3p 7 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+tRNA-Lys-CTT-chr15-5 89 +tRNA-Lys-CTT-chr16-1 2 +tRNA-Lys-CTT-chr7-30 38 +tRNA-Lys-TTT-1-1 154 +tRNA-Lys-TTT-12-1 2 +tRNA-Lys-TTT-13-1 1 +tRNA-Lys-TTT-14-1 91 +tRNA-Lys-TTT-15-1 2 +tRNA-Lys-TTT-2-1 163 +tRNA-Lys-TTT-3-1 1272 +tRNA-Lys-TTT-3-2 749 +tRNA-Lys-TTT-3-3 508 +tRNA-Lys-TTT-3-4 750 +tRNA-Lys-TTT-3-5 627 +tRNA-Lys-TTT-4-1 358 +tRNA-Lys-TTT-5-1 298 +tRNA-Lys-TTT-6-1 111 +tRNA-Lys-TTT-7-1 342 +tRNA-Lys-TTT-8-1 5 +tRNA-Lys-TTT-9-1 3 +tRNA-Met-CAT-1-1 1898 +tRNA-Met-CAT-2-1 4 +tRNA-Met-CAT-3-1 161 +tRNA-Met-CAT-3-2 426 +tRNA-Met-CAT-4-1 17 +tRNA-Met-CAT-4-2 13 +tRNA-Met-CAT-4-3 15 +tRNA-Met-CAT-6-1 583 +tRNA-Met-CAT-7-1 6 +tRNA-Met-CAT-chr6-80 1 +tRNA-Phe-GAA-10-1 8 +tRNA-Phe-GAA-1-1 75 +tRNA-Phe-GAA-1-2 190 +tRNA-Phe-GAA-1-3 58 +tRNA-Phe-GAA-1-4 199 +tRNA-Phe-GAA-1-5 241 +tRNA-Phe-GAA-1-6 91 +tRNA-Phe-GAA-2-1 66 +tRNA-Phe-GAA-3-1 402 +tRNA-Phe-GAA-4-1 1 +tRNA-Phe-GAA-5-1 8 +tRNA-Phe-GAA-6-1 2 +tRNA-Phe-GAA-8-1 2 +tRNA-Phe-GAA-9-1 8 +tRNA-Pro-AGG-1-1 566 +tRNA-Pro-AGG-2-1 606 +tRNA-Pro-AGG-2-2 318 +tRNA-Pro-AGG-2-3 326 +tRNA-Pro-AGG-2-4 705 +tRNA-Pro-AGG-2-5 672 +tRNA-Pro-AGG-2-6 651 +tRNA-Pro-AGG-2-7 663 +tRNA-Pro-AGG-2-8 370 +tRNA-Pro-AGG-3-1 2 +tRNA-Pro-CGG-1-1 1365 +tRNA-Pro-CGG-1-2 1226 +tRNA-Pro-CGG-1-3 1887 +tRNA-Pro-CGG-2-1 1365 +tRNA-Pro-TGG-1-1 177 +tRNA-Pro-TGG-2-1 2545 +tRNA-Pro-TGG-3-1 1593 +tRNA-Pro-TGG-3-2 784 +tRNA-Pro-TGG-3-3 718 +tRNA-Pro-TGG-3-4 4412 +tRNA-Pro-TGG-3-5 3475 +tRNA-SeC-TCA-1-1 3881 +tRNA-SeC-TCA-2-1 72 +tRNA-SeC-TCA-3-1 1 +tRNA-Ser-ACT-1-1 75 +tRNA-Ser-AGA-1-1 97 +tRNA-Ser-AGA-2-1 155 +tRNA-Ser-AGA-2-2 89 +tRNA-Ser-AGA-2-3 97 +tRNA-Ser-AGA-2-4 92 +tRNA-Ser-AGA-2-5 92 +tRNA-Ser-AGA-2-6 138 +tRNA-Ser-AGA-3-1 81 +tRNA-Ser-AGA-4-1 164 +tRNA-Ser-AGA-5-1 2 +tRNA-Ser-AGA-6-1 1 +tRNA-Ser-CGA-1-1 736 +tRNA-Ser-CGA-2-1 546 +tRNA-Ser-CGA-3-1 988 +tRNA-Ser-CGA-4-1 612 +tRNA-Ser-GCT-1-1 42 +tRNA-Ser-GCT-2-1 135 +tRNA-Ser-GCT-3-1 547 +tRNA-Ser-GCT-4-1 649 +tRNA-Ser-GCT-4-2 705 +tRNA-Ser-GCT-4-3 185 +tRNA-Ser-GCT-5-1 199 +tRNA-Ser-GCT-6-1 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a/smRNA-seq/count/ZR751.srt.annotated.cnt b/smRNA-seq/count/ZR751.srt.annotated.cnt new file mode 100644 index 0000000000000000000000000000000000000000..777d78cdee508ca10cd6bad6939ac2c045bcf8d9 --- /dev/null +++ b/smRNA-seq/count/ZR751.srt.annotated.cnt @@ -0,0 +1,1020 @@ +14q(I-3) 1 +14q(II-12) 3 +ACA1 262 +ACA10 252 +ACA11 21 +ACA12 75 +ACA13 479 +ACA14a 8 +ACA14b 580 +ACA15 25 +ACA16 18 +ACA17 617 +ACA18 320 +ACA19 443 +ACA20 597 +ACA21 1296 +ACA22 25 +ACA23 199 +ACA24 212 +ACA25 290 +ACA26 865 +ACA27 124 +ACA28 302 +ACA2a 44 +ACA2b 75 +ACA3 860 +ACA30 114 +ACA31 587 +ACA3-2 889 +ACA32 221 +ACA33 251 +ACA34 22 +ACA35 32 +ACA36 80 +ACA36B 176 +ACA37 163 +ACA38 16 +ACA39 329 +ACA4 476 +ACA40 424 +ACA41 106 +ACA42 824 +ACA43 109 +ACA44 255 +ACA45 68 +ACA46 405 +ACA47 7 +ACA48 288 +ACA49 29 +ACA5 224 +ACA50 43 +ACA51 279 +ACA52 25 +ACA53 68 +ACA54 115 +ACA55 199 +ACA56 75 +ACA57 54 +ACA58 374 +ACA59 24 +ACA59B 6 +ACA5b 1 +ACA5c 161 +ACA6 358 +ACA60 127 +ACA61 397 +ACA62 795 +ACA63 31 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