{"id":866,"date":"2013-04-11T09:36:58","date_gmt":"2013-04-11T01:36:58","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=866"},"modified":"2013-04-16T09:58:52","modified_gmt":"2013-04-16T01:58:52","slug":"myrna%e7%9a%84%e5%ae%89%e8%a3%85%e4%b8%8e%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=866","title":{"rendered":"myrna\u672c\u5730\u5316\u7684\u5b89\u88c5\u4e0e\u4f7f\u7528"},"content":{"rendered":"

\u4e00. Myrna\u7684\u7b80\u4ecb<\/h1>\n

Myrna<\/a>\u4e3b\u8981\u7528\u9014\u662f\uff0c\u4f7f\u7528RNA-seq\u6570\u636e\u6765\u8ba1\u7b97\u57fa\u56e0\u5dee\u5f02\u8868\u8fbe\u3002
\nMyrna\u7684\u8fd0\u884c\u6b65\u9aa4\u662f\uff1a<\/p>\n

1. \u5c06reads\u8fdb\u884c\u9884\u5904\u7406; \r\n2. \u4f7f\u7528Bowtie\u5c06reads\u6bd4\u5bf9\u5230\u53c2\u8003\u5e8f\u5217\u4e0a; \r\n3. \u4f7f\u7528R\/Bioconductor\u5c06\u6bd4\u5bf9\u7ed3\u679c\u5b9a\u4f4d\u5230genes\u4e0a; \r\n4. \u6807\u51c6\u5316\u57fa\u56e0\u7684\u6bd4\u5bf9\u6570; \r\n5. \u8ba1\u7b97\u5dee\u5f02\u8868\u8fbe\u7684\u7edf\u8ba1\u6570\u636e; \r\n6. \u5c06\u7ed3\u679c\u7ed8\u5236\u51fa\u56fe\u3002<\/pre>\n
Myrna\u6709\u4e09\u79cd\u4f7f\u7528\u65b9\u5f0f:<\/p>\n
1. \u5728\u4e91\u7aef\u4f7f\u7528\uff0cAmazon's Elastic MapReduce service\uff1b \r\n2. \u5728 hadoop \u96c6\u7fa4\u4e0a\u4f7f\u7528; \r\n3. \u5728\u5355\u72ec\u7684\u4e00\u53f0\u8ba1\u7b97\u673a\u4e0a\u4f7f\u7528\u3002<\/pre>\n
\u53c2\u8003\u6587\u732e(2010)\uff1aCloud-scale RNA-sequencing differential expression analysis with Myrna<\/a>
\n\u53ea\u6709\u8bfb\u8be5\u6587\u732e\u624d\u80fd\u5168\u9762\u4e86\u89e3Myrna.<\/p>\n
\u4e8c. Myrna\u7684\u5b89\u88c5<\/h1>\n
1. \u4e0b\u8f7dMyrna\u5e76\u5b89\u88c5<\/h2>\n
cd \/home\/chenlianfu\/programs\/\r\n$ wget http:\/\/nchc.dl.sourceforge.net\/project\/bowtie-bio\/myrna\/1.2.0\/myrna-1.2.0.zip\r\n$ unzip myrna-1.2.0.zip\r\n\r\n\u8bbe\u7f6eMyrna\u7684\u73af\u5883\u53d8\u91cfMYRNA_HOME:\r\n$ vim ~\/.bashrc\r\nexport MYRNA_HOME=\/home\/chenlianfu\/programs\/myrna-1.2.0<\/pre>\n
2. \u5b89\u88c5bowtie<\/h2>\n
\u5b89\u88c5\u5b8cbowtie\uff0c\u518d\u5c06\u5176\u6267\u884c\u7a0b\u5e8fbin\u76ee\u5f55\u6dfb\u52a0\u5230\u73af\u5883\u53d8\u91cfMYRNA_BOWTIE_HOME\u3002\u6216\u8005\u5728\u8fd0\u884c\u7a0b\u5e8f\u65f6\u5019\u4f7f\u7528\u53c2\u6570 –bowtie<\/p>\n
\u8bbe\u7f6eMyrna\u7684\u73af\u5883\u53d8\u91cfMYRNA_BOWTIE_HOME:\r\n$ vim ~\/.bashrc\r\nexport MYRNA_BOWTIE_HOME=\/home\/chenlianfu\/programs\/bowtie-1.0.0\/<\/pre>\n
3. \u5b89\u88c5R\uff0cBioconductor\u53ca\u5fc5\u987b\u7684\u5305<\/h2>\n
\u672c\u8f6f\u4ef6(\u7248\u672c1.20)\u7684\u4f7f\u7528\u5fc5\u987b\u4f7f\u7528R2.14\uff0c\u9ad8\u7248\u672c\u7684R\u8fd8\u4e0d\u517c\u5bb9\u3002\u6545\u4f7f\u7528Myrna\u81ea\u5e26\u7684\u4e00\u4e2a\u811a\u672c\u6765\u4e0b\u8f7dR2.14\u5e76\u5b89\u88c5\u3002<\/p>\n
# R\r\n\r\n\u5b89\u88c5R\u5305 lmtest \u548c multicore:\r\n> install.packages(\"lmtest\")\r\n> install.packages(\"multicore\")\r\n\r\n\u5b89\u88c5Bioconductor:\r\n> source(\"http:\/\/bioconductor.org\/biocLite.R\")\r\n> biocLite()\r\n\r\n\u5b89\u88c5Bioconductor\u5305 IRanges,geneplotter,BiocGenerics \u548c biomaRt:\r\n> source(\"http:\/\/bioconductor.org\/biocLite.R\")\r\n> biocLite(\"IRanges\")\r\n> biocLite(\"geneplotter\")\r\n> biocLite(\"BiocGenerics\")\r\n> biocLite(\"biomaRt\")\r\n\r\n\u8bbe\u7f6eMyrna\u7684\u73af\u5883\u53d8\u91cfMYRNA_RHOME(\u5305\u542bbin\/R\u548cbin\/Rscript):\r\nvim ~\/.bashrc\r\nexport MYRNA_RHOME=\/usr\/local\/<\/pre>\n
4. \u5b89\u88c5SRA toolkit<\/h2>\n
\u5982\u679c\u8f93\u5165Myrna\u7684\u8f6f\u4ef6\u662f.sra\u683c\u5f0f\uff0c\u5219\u9700\u8981SRA toolkit\u4e2d\u7684\u7a0b\u5e8f fastq-dump \u4e86\u3002\u5b89\u88c5\u73a9 SRA toolkit \u540e\uff0c\u518d\u8bbe\u7f6eMyrna\u7684\u73af\u5883\u53d8\u91cf\uff1a<\/p>\n
$ vim ~\/.bashrc\r\nexport MYRNA_SRATOOLKIT_HOME=\/home\/chenlianfu\/programs\/sratoolkit.2.3.1-centos_linux64\/bin\/<\/pre>\n
5. \u6d4b\u8bd5\u672c\u5730\u5316\u8fd0\u884c\u7a0b\u5e8f<\/h2>\n
\u4f7f\u7528\u672c\u5730\u5316\u8fd0\u884c\u7a0b\u5e8fmyrna_local\u6765\u8fdb\u884c\u6d4b\u8bd5\uff0c\u901a\u8fc7\u8868\u793a\u5b89\u88c5\u6210\u529f\u3002<\/p>\n
$ $MYRNA_HOME\/myrna_local --test\r\n...\r\nPASSED install test<\/pre>\n
6. \u8bbe\u7f6e\u7684\u4e00\u4e9b\u73af\u5883\u53d8\u91cf<\/h2>\n
$ vim ~\/.bashrc\r\nexport MYRNA_BOWTIE_HOME=\/home\/chenlianfu\/programs\/bowtie-1.0.0\/\r\nexport MYRNA_HOME=\/home\/chenlianfu\/programs\/myrna-1.2.0\r\nexport MYRNA_RHOME=\/usr\/local\/\r\nexport MYRNA_SRATOOLKIT_HOME=\/home\/chenlianfu\/programs\/sratoolkit.2.3.1-centos_linux64\/bin\/\r\nexport MYRNA_REFS=\/home\/chenlianfu\/programs\/myrna-1.2.0\/reftools\/<\/pre>\n
\u4e09. Myrna\u7684\u4f7f\u7528<\/h1>\n
1. \u672c\u5730\u5316\u8fd0\u884c\u7a0b\u5e8f\u7684\u4f7f\u7528\u53c2\u6570\uff1a<\/h2>\n
--reference <path><\/span>\r\n    \u53c2\u8003\u5e8f\u5217\u7684\u6587\u4ef6\u5939\u3002\u8be5\u6587\u4ef6\u5939\u7531\u4e00\u4e2a\u53c2\u8003\u5e8f\u5217jar\u6587\u4ef6\u4f7f\u7528unzip\u89e3\u538b\u7f29\u51fa\u6765\u7684\uff0c\u91cc\u9762\u4e3b\r\n\u8981\u5305\u62ec\u4e24\u4e2a\u5b50\u6587\u4ef6\u5939\uff1a1.\"index\":\u91cc\u9762\u5305\u542bbowtie-bulid\u4ea7\u751f\u7684index\u6587\u4ef6\uff1b2.\"ival\r\ns\":\u91cc\u9762\u5305\u542bgene\u7684\u6ce8\u91ca\u4fe1\u606f\u3002\r\n\r\n--input <path><\/span>\r\n    \u8f93\u5165\u7684\u6587\u4ef6\u6216\u6587\u4ef6\u5939\u8def\u5f84\u3002\u5982\u679c\u4e0d\u6307\u5b9a--preprocess \u53c2\u6570\uff0c\u5219\u8be5\u53c2\u6570\u540e\u63a5\u7684\u662f\u4e00\u4e2a\r\n\u6587\u4ef6\u5939\uff0c\u8be5\u6587\u4ef6\u5939\u5305\u542b\u4e86reads\u7684\u9884\u5904\u7406\u7ed3\u679c\uff0c\u5373 --preprocess-output \u7684\u8f93\u51fa\u7ed3\u679c\uff1b\r\n\u5982\u679c\u6307\u5b9a\u4e86 --preprocess \u53c2\u6570\uff0c\u5219\u662f\u4e00\u4e2a\u6587\u672c\u6587\u4ef6\uff0c\u5185\u5bb9\u4e3a\u8f93\u5165\u7684\u5e8f\u5217\u6587\u4ef6\u7684\u4e00\u4e2a\u6e05\u5355\r\n(Labeled manifest files)\u3002\u8be5\u6587\u4ef6\u63cf\u8ff0\u4e86\u8f93\u5165\u5e8f\u5217\u6587\u4ef6\u548c\u6837\u672c\u7684\u4fe1\u606f\u3002\u5e8f\u5217\u6587\u4ef6\u662f\r\nFASTQ\u6216sra\u683c\u5f0f\u6587\u4ef6\uff0cFASTQ\u683c\u5f0f\u53ef\u4ee5\u662fgzip\u6216bzip2\u538b\u7f29\u3002\u8be5\u6587\u4ef6\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u6d4b\u5e8f\r\n\u7684\u7ed3\u679c\uff0c\u662f\u4ee5\u4e0b\u662f unpaired reads \u548c paired reads \u7684\u4e66\u5199\u65b9\u6cd5\uff1a\r\n<URL>(tab)<Optional MD5>(tab)<Sample label>\r\n<URL 1>(tab)<Optional MD5 1>(tab)<URL 2>(tab)<Optional MD5 2>(tab)<Sample label>\r\n\r\n\u5176\u4e2dURL\u662f\u6d4b\u5e8f\u7ed3\u679c\u6587\u4ef6\u7684\u8def\u5f84\uff0c\u53ef\u4ee5\u662fftp\u7ad9\u70b9\u4e0a\u7684\u6587\u4ef6\uff1bMD5\u662f\u53ef\u9009\u7684\uff0c\u4ee5\u5229\u4e8e\u4e0b\u8f7d\u6587\u4ef6\u540e\r\n\u7528\u4e8e\u6587\u4ef6\u7684\u5b8c\u6574\u5ea6\u68c0\u9a8c\uff0c\u82e5\u4e0d\u60f3\u8fdb\u884c\u68c0\u9a8c\uff0c\u5219\u8bbe\u7f6e\u4e3a0\uff1b<Sample label>\u7684\u5199\u6cd5\u4e3a\uff1a\r\n<Group ID>-<BioRep ID>-<TechRep ID>\r\n\r\n\u5176\u4e2d\uff0cGroup ID \u662f\u6837\u54c1\u7684\u540d\u79f0\uff1bBioRep ID\u662f\u751f\u7269\u5b66\u91cd\u590d\u7684\u4ee3\u53f7\uff1bTechRep ID\u662f\u6280\u672f\u6027\r\n\u91cd\u590d\u7684\u4ee3\u53f7\u3002\u6bd4\u5982\uff1a\r\nTumor-Subject1-Lane1\r\nTumor-Subject1-Lane2\r\nTumor-Subject2-Lane1\r\nTumor-Subject2-Lane2\r\nNormal-Subject1-Lane1\r\nNormal-Subject1-Lane2\r\nNormal-Subject2-Lane1\r\nNormal-Subject2-Lane2\r\n\r\n--output <path><\/span>\r\n    \u8f93\u51fa\u6587\u4ef6\u7684\u8def\u5f84\u3002\u5982\u679c --just-preprocess \u53c2\u6570\u7ed9\u5b9a\uff0c\u5219\u53ea\u662f\u5bf9reads\u6587\u4ef6\u8fdb\u884c\u9884\r\n\u5904\u7406\uff0c\u7ed9\u51fa\u7ed3\u679c\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u5219\u662f\u8f93\u51fa\u6700\u7ec8\u7ed3\u679c\uff1a\u4e00\u7cfb\u5217\u7684\u8868\u683c\uff0c\u56fe\u548c\u6bd4\u5bf9\u6587\u4ef6\u3002\r\n\r\n--intermediate <path>  default: \/tmp\/myrna\/intermediate\/<PID><\/span>\r\n    \u4e2d\u95f4\u7ed3\u679c\u6587\u4ef6\u5b58\u653e\u7684\u4e34\u65f6\u8def\u5f84\u3002\u5982\u679c\u6307\u5b9a\u4e86 --keep-intermediates \u6216 --keep-\r\nall\u53c2\u6570\uff0c\u5219\u8be5\u6587\u4ef6\u5219\u4f1a\u4e00\u76f4\u5b58\u5728\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u4f1a\u4f7f\u7528\u5b8c\u6bd5\u540e\u5220\u9664\u3002\r\n\r\n--preprocess-output <path><\/span>\r\n    \u5bf9reads\u8fdb\u884c\u9884\u5904\u7406\u7684\u8f93\u51fa\u8def\u5f84\u3002\u7531\u4e8e\u5bf9reads\u7684\u9884\u5904\u7406\u4f1a\u6d88\u8017\u5f88\u591a\u65f6\u95f4\uff0c\u56e0\u6b64\u4fdd\u7559\u6570\u636e\r\n\u7684\u9884\u5904\u7406\u7ed3\u679c\uff0c\u5bf9\u518d\u6b21\u8fd0\u884c\u7a0b\u5e8f\u6765\u8bf4\uff0c\u53ef\u4ee5\u8282\u7ea6\u5f88\u591a\u65f6\u95f4\u3002\r\n\r\n--keep-intermediates <path><\/span>\r\n    \u4fdd\u7559\u7a0b\u5e8f\u8fd0\u884c\u4e2d\u751f\u6210\u7684\u7ed3\u679c\u6587\u4ef6\u5939\u548c\u6587\u4ef6\uff0c\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u8fd9\u4e9b\u6587\u4ef6\u4f1a\u88ab\u5c3d\u5feb\u7684\u81ea\u52a8\u5220\u9664\u3002\r\n\r\n--keep-all<\/span>\r\n    \u4fdd\u7559\u6240\u6709\u7684\u4e34\u65f6\u6587\u4ef6\uff0c\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u8fd9\u4e9b\u6587\u4ef6\u4f1a\u88ab\u5c3d\u5feb\u7684\u81ea\u52a8\u5220\u9664\u3002\r\n\r\n--cpus <int>  default: 1<\/span>\r\n   \u8bbe\u5b9a\u7a0b\u5e8f\u8fd0\u884c\u4f7f\u7528\u7684CPU\u7ebf\u7a0b\u6570\u3002\r\n\r\n--bowtie <path><\/span>\r\n    \u8bbe\u5b9aBowtie\u7684\u8def\u5f84\uff0c\u4ee5\u8fd0\u7528bowtie\u8fdb\u884c\u6bd4\u5bf9\u7684\u6b65\u9aa4\uff0c\u8be5\u53c2\u6570\u4f18\u5148\u4e8e\u73af\u5883\u53d8\u91cfMYRNA_\r\nBOWTIE_HOME\uff0c$MYRNA_HOME\/bin\u7684\u5b50\u76ee\u5f55\uff0c\u4ee5\u53ca PATH\u3002\r\n\r\n--fastq-dump <path><\/span>\r\n    \u8bbe\u5b9a SRA toolkit \u4e2d\u7684 fastq-dump \u7a0b\u5e8f\u7684\u4f4d\u7f6e\uff0c\u4f18\u5148\u4e8ePAHT\u3002\r\n\r\n--Rhome <path><\/span>\r\n    \u8bbe\u5b9aR\u548cR\/Bioconductor\u5b89\u88c5\u7a0b\u5e8f\u7684\u4f4d\u7f6e\uff0c\u8be5\u76ee\u5f55\u5305\u62ec bin\/R \u548c bin\/Rscript,\r\n\u4f18\u5148\u4e8e\u73af\u5883\u53d8\u91cfMYRNA_RHOME\u548cPATH\u3002<\/pre>\n
2. emr, hadhoop \u548c local\u8fd0\u884c\u7684\u5171\u540c\u53c2\u6570<\/h2>\n
--quality { phred33 | phred64 | solexa64 }  default: phred33<\/span>\r\n    \u8bbe\u7f6e\u8f93\u5165reads\u7684\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\u3002phred33:\u8f93\u5165\u7684\u78b1\u57fa\u8d28\u91cf\u7b49\u4e8eASCII\u7801\u503c\u52a0\u4e0a33;\u6700\r\n\u4f4e\u78b1\u57fa\u8d28\u91cf\u662f\u201c#\u201d. phred64:\u8f93\u5165\u7684\u78b1\u57fa\u8d28\u91cf\u7b49\u4e8eASCII\u7801\u503c\u52a0\u4e0a64;\u6700\u4f4e\u78b1\u57fa\u8d28\u91cf\u662f\u201cB\u201d. \r\n\r\n--preprocess<\/span>\r\n    \u5f53 --input \u7684\u53c2\u6570\u662f\u4e00\u4e2a\u6587\u672c\u6587\u4ef6\uff08\u542b\u6709\u8f93\u5165\u5e8f\u5217\u4fe1\u606f\u7684\u6e05\u5355\uff09\u65f6\uff0c\u5219\u5fc5\u987b\u52a0\u5165\u8be5\u53c2\u6570\r\n\uff1b\u8be5\u53c2\u6570\u6307\u5b9a\u51fa\u4e86\u6587\u672c\u6587\u4ef6\u4e2d\u7684\u5e8f\u5217\u4fe1\u606f\u6765\uff0cMyrna\u5219\u8fdb\u884c\u8fd9\u4e9breads\u7684\u9884\u5904\u7406\uff0c\u5c06\u751f\u6210\u7684\u9884\u5904\r\n\u7406reads\u7ed3\u679c\u8f93\u51fa\u5230 --preprocess-output \u6307\u5b9a\u7684\u6587\u4ef6\u5939\uff1b\u5982\u679c\u4e0d\u6307\u5b9a--preprocess\r\n-output\u53c2\u6570\uff0c\u5219\u8f93\u51fa\u5230 --intermediate \u6307\u5b9a\u7684\u6587\u4ef6\u5939\u3002\r\n\r\n--just-preprocess<\/span>\r\n    \u548c --preprocess \u53c2\u6570\u7c7b\u4f3c\uff0c\u4f46\u4e0d\u540c\u7684\u662f\u8fdb\u884creads\u9884\u5904\u7406\u540e\uff0c\u5373\u505c\u6b62pipeline\u7684\r\n\u8fd0\u884c\uff0c\u5e76\u5c06\u7ed3\u679c\u8f93\u51fa\u5230 --output\u6307\u5b9a\u7684\u6587\u4ef6\u5939\u3002\r\n\r\n--just-align<\/span>\r\n    \u4e0d\u5c06Myrna\u7684pipeline\u8fd0\u884c\u5230\u5e95\uff0c\u53ea\u662f\u8fd0\u884c\u5230\u6bd4\u5bf9\u7ed3\u675f\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u653e\u5230 --output \r\n\u53c2\u6570\u6307\u5b9a\u7684URL.\r\n\r\n--resume-align<\/span>\r\n    \u4f7f\u7528\u6b64\u547d\u4ee4\u6765\u8fd0\u884c\u4e0a\u4e00\u4e2a\u547d\u4ee4\uff08\u6bd4\u5bf9\u5b8c\u6bd5\uff09\u8fc7\u540e\u7684\u9636\u6bb5\u3002 \u6b64\u65f6 --input \u7684\u53c2\u6570\u5219\u662f\u4e0a\r\n\u4e00\u4e2a\u547d\u4ee4\u4e2d --output\u7684URL.\r\n\r\n--bowtie-args \"<args>\"  default: -m 1<\/span>\r\n    \u8bbe\u7f6ebowtie\u7684\u53c2\u6570\u3002\r\n\r\n--discard-reads <fraction>  default: 0.0<\/span>\r\n    \u4e22\u5f03\u4e00\u5b9a\u6bd4\u4f8b\u8f93\u7684reads\u6765\u8fdb\u884c\u7a0b\u5e8f\u7684\u8fd0\u884c\u3002\u6bd4\u5982 0.5 \u5219\u4ee3\u8868\u4e22\u5f0350%\u7684reads\u3002\u8be5\u53c2\r\n\u6570\u5e94\u7528\u4e8e\u6240\u6709\u8f93\u5165\u7684reads\u3002\u5bf9\u4e8e\u7a0b\u5e8f\u7684\u8c03\u8bd5\u6bd4\u8f83\u6709\u7528\u3002\r\n\r\n--influence <int>  default: 1<\/span>\r\n    \u4e00\u4e2aread\u7684\"influence\"\u957f\u5ea6\u3002\u548c\u4e0b\u97623\u4e2a\u53c2\u6570\u6709\u5173\u7cfb\u3002\r\n\r\n--from3prime<\/span>\r\n    \u8bbe\u5b9a\u4fee\u526a\u8fc7\u540e\u7684reads\u4ece3'\u7aef\u5f00\u59cb\u8861\u91cf\u5176\"influence\"\u3002\u6b64\u53c2\u6570\u662f\u9ed8\u8ba4\u8bbe\u7f6e\uff0c\u548c\u4e0b2\u4e2a\r\n\u53c2\u6570\u662f\u51b2\u7a81\u7684\uff0c\u4e09\u9009\u4e00\u3002\r\n\r\n--from5prime<\/span>\r\n    \u8bbe\u5b9a\u4fee\u526a\u8fc7\u540e\u7684reads\u4ece5'\u7aef\u5f00\u59cb\u8861\u91cf\u5176\"influence\"\u3002\r\n\r\n--from-middle<\/span>\r\n    \u8bbe\u5b9a\u4fee\u526a\u8fc7\u540e\u7684reads\u4ece\u4e2d\u95f4\u5f00\u59cb\u8861\u91cf\u5176\"influence\"\u3002\r\n\r\n--top <int>  default:50<\/span>\r\n    \u5c06genes\u6309p\u503c\u4ece\u5c0f\u5230\u5927\u6392\u5e8f\uff0cMyrna\u5c06\u62a5\u544a\u51fa\u524d\u4e00\u5b9a\u6570\u76ee\u7684genes\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\u9ed8\u8ba4\u662f\r\n50\u4e2agenes\u3002\r\n\r\n--family { poisson | gaussian }  default: poisson<\/span>\r\n    \u8bbe\u5b9a\u68c0\u6d4bgene\u7684\u5dee\u5f02\u8868\u8fbe\u7684\u7edf\u8ba1\u65b9\u6cd5\u3002possion\u9002\u5408\u4e8e\u6837\u672c<=10\u4e2a\uff1bgaussian\u9002\u5408\u4e8e\r\n\u6837\u672c\u6570>10\u3002\u5f53\u7136\u8fd9\u4e0d\u662f\u786c\u6027\u89c4\u5b9a\uff0c\u5177\u4f53\u8fd8\u8981\u7528\u5b9e\u9a8c\u9a8c\u8bc1\u3002\u5f53 --nulls \u53c2\u6570\u662f 0 \u6216\u8005 \u6ca1\u6709\r\n\u7ed9\u51fa\u65f6\uff0c\u5219\u4f7f\u7528\u6b64\u53c2\u6570\u4e2d\u7684\u6a21\u578b\u6765\u4f5c\u53c2\u6570\u68c0\u9a8c(parameric statistical model)\uff0c\u8ba1\u7b97\r\n\u51fap-value.\u5f53 --nulls\u53c2\u6570\u5927\u4e8e0\uff0c\u5219\u4f7f\u7528permutation test\u6765\u8ba1\u7b97p-value.\r\n\r\n--normalize { total | median | upper-quartile }<\/span>\r\n    Each count (or pooled count) is \"normalized\" according to a \r\nper-label baseline normalization factor.\r\n\r\n--gene-footprint { union | intersect }  default: intersect<\/span>\r\n    \u8ba1\u7b97\u6bd4\u5bf9\u548cgenges\u7684\u5173\u8054\u65f6\u6240\u4f7f\u7528\u7684 gene footprint\u3002intersect \u548c union \r\n\u5206\u522b\u5bf9\u5e94\u8fd9reference\u6587\u4ef6\u5939\u4e2d\u7684ivals\u5b50\u6587\u4ef6\u5939\u4e2d\u7684ui\u548cun\u6587\u4ef6\u5939\uff1b\u5176\u4e2dun\u5bf9\u5e94\u7684\u57fa\u56e0\u533a\r\n\u8981\u6bd4ui\u591a\uff0c\u5e76\u4e14un\u7684\u57fa\u56e0\u533a\u5305\u542b\u4e86ui\u7684\uff0c\u4e2a\u4eba\u63a8\u6d4b\u53ef\u80fd\u662fun\u5305\u542b\u4e865'\u7aef\u548c3'\u7aef\u975e\u7ffb\u8bd1\u533a\u3002\r\nunion: \u5c06\u4e00\u4e2a\u6bd4\u5bf9\u7ed3\u679c\u6307\u5411\u67d0\u4e00\u4e2agene\u7684\u5fc5\u8981\u6761\u4ef6\u662f\uff0cread\u7684\"influence\"(\u9ed8\u8ba4\u4e0b\u662f\r\n\u4ece3'\u7aef\u5f00\u59cb)\u6709\u4e00\u4e2a\u78b1\u57fa\u548c\u4e00\u4e2agene\u4efb\u610f\u7684(any)transcripts\u91cd\u53e0\uff1bintersect: \u5c06\r\n\u4e00\u4e2a\u6bd4\u5bf9\u7ed3\u679c\u6307\u5411\u67d0\u4e00\u4e2agene\u7684\u5fc5\u8981\u6761\u4ef6\u662f\uff0cread\u7684\"influence\"(\u9ed8\u8ba4\u4e0b\u662f\u4ece3'\u7aef)\u6709\u4e00\r\n\u4e2a\u78b1\u57fa\u548c\u4e00\u4e2agene\u6240\u6709\u7684(all)\u7684transcripts\u91cd\u53e0\u3002\u6211\u4e2a\u4eba\u7684\u7406\u89e3\uff0c\u901a\u4fd7\u6765\u8bb2\uff1a\u4ee5\u4e0a\u6570\u4e2a\r\n\u53c2\u6570\u7684\u76ee\u7684\u662f\u8ba1\u7b97\u6bd4\u5bf9\u5230gene\u4e0a\u7684reads\u7684\u6570\u76ee\u3002\u6839\u636e\u6bd4\u5bf9\u7ed3\u679c\uff0c\u9ed8\u8ba4\u5c06reads\u4ece3'\u7aef\u5f00\u59cb\r\n\u8ba1\u7b97\uff0c\u5982\u679c\u6bd4\u5bf9\u4e0areads\u6709\u4e00\u4e2a\u78b1\u57fa\u548c\u4e00\u4e2agene\u7684\u4e00\u4e2a\u5916\u663e\u5b50\u91cd\u53e0\uff0c\u5219\u5728union\u6a21\u5f0f\u4e0b\u8fd9\u4e2a\r\ngene\u5219\u53ef\u4ee5\u5f97\u5230\u4e00\u4e2aread\u6bd4\u5bf9\u7ed3\u679c\uff1b\u800c\u5728intersect\u6a21\u5f0f\u4e0b\uff0c\u8fd9\u4e2areads\u5fc5\u987b\u548c\u8be5gene\u6240\r\n\u6709\u7684\u5916\u663e\u5b50\u6709\u4e00\u4e2a\u78b1\u57fa\u7684\u91cd\u53e0\uff0c\u5219\u8be5gene\u624d\u80fd\u5f97\u5230\u4e00\u4e2aread\u6bd4\u5bf9\u7ed3\u679c\u3002\u53ef\u89c1intersect\u8981\u6c42\r\nread\u8d2f\u7a7f\u6574\u4e2agene\u624d\u884c\u80fd\u5f97\u5230\u6bd4\u5bf9\u5230gene\u7684\u6570\u76ee\uff1b\u56e0\u6b64\uff0c\u5bf9\u4e8eshort reads\u8fdb\u884c\u57fa\u56e0\u8868\u8fbe\r\n\u91cf\u8ba1\u7b97\u7684\u65f6\u5019\uff0c\u5219\u9700\u8981\u9009union\u6a21\u5f0f\uff0c\u4e0d\u80fd\u9009\u9ed8\u8ba4\u7684\u6a21\u5f0f\u3002\r\n\r\n--paired-ttest<\/span>\r\n    \u5982\u679c\u8bbe\u5b9a\u6b64\u503c\uff0c\u5219\u8868\u793a\uff1a 1, \u662f\u5bf92\u4e2a\u6837\u4f5c\u6bd4\u8f83\uff1b 2, \u8fd92\u4e2a\u6837\u7684\u751f\u7269\u5b66\u91cd\u590d\u5fc5\u987b\u8981\u5339\r\n\u914d\u3002\u5f53\u8be5\u53c2\u6570\u4f7f\u7528\u65f6\uff0c\u5c06\u5bf9\u4e24\u4e2a\u6837\u4f5ct\u68c0\u9a8c\u3002\r\n\r\n--nulls <int><\/span>\r\n    Set the number of null statistics generated per gene to <int>.\r\n A null statistic for a gene is calculated by permuting the sample\r\n labels for the counts and normalization factors, then re-calcula-\r\n-ting the statistical test. \u5982\u679c<int>\u662f\u4e00\u4e2a\u975e0\u7684\u6570\uff0c\u5219p-values\u7531permu-\r\n-tation test\u5f97\u51fa\uff1b\u5426\u5219\uff0cp-values\u7531\u53c2\u6570\u68c0\u9a8c\u6a21\u578b(parametric statistical \r\nmodel)\u8ba1\u7b97\u51fa\u3002\r\n\r\n--truncate <int><\/span>\r\n    \u5c06\u6240\u6709\u7684reads\u90fd\u4ece3'\u7aef\u5f00\u59cb\u4fee\u526a\uff0c\u76f4\u5230\u8be5\u53c2\u6570\u8bbe\u5b9a\u7684\u957f\u5ea6\uff1b\u5c0f\u4e8e\u8be5\u957f\u5ea6\u7684reads\u4f9d\u7136\r\n\u4fdd\u7559\u3002\r\n\r\n--truncate-discard <int><\/span>\r\n    \u5c06\u6240\u6709\u7684reads\u90fd\u4ece3'\u7aef\u5f00\u59cb\u4fee\u526a\uff0c\u76f4\u5230\u8be5\u53c2\u6570\u8bbe\u5b9a\u7684\u957f\u5ea6\uff1b\u800c\u5c0f\u4e8e\u8be5\u957f\u5ea6\u7684reads\u5168\r\n\u90e8\u5254\u9664\u3002\r\n\r\n--ditch-alignments<\/span>\r\n    \u4e0d\u8f93\u51fa\u6bd4\u5bf9\u7ed3\u679c\u548c\u56fe\u5f62\u7ed3\u679c\uff1b\u4f9d\u7136\u62a5\u544a\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\uff0cp-values\u548c\u76f8\u5173\u7684\u56fe\u5f62\u7ed3\u679c\u3002\r\n\r\n--discard-mate <int><\/span>\r\n    \u5bf9\u4e8e paired-end reads\uff0c\u53bb\u6389\u5176\u4e2d\u4e00\u7aef\u7684\u5e8f\u5217( 1 \u6216 2 )\u518d\u6765\u8fdb\u884c\u6bd4\u5bf9\u3002\u8fd9\u5bf9\u4e8e\r\n\u4e00\u4e9b\u6570\u636e\u96c6\u7684\u6bd4\u8f83\u6709\u7528\uff0c\u6bd4\u5982\u6570\u636e\u96c6\u4e2d\u540c\u65f6\u6709 paired reads \u548c unpaired reads\u65f6\u3002\r\n\r\n--pool-reps<\/span>\r\n    \u5c06\u6240\u6709\u7684\u91cd\u590d\uff0c\u5305\u62ec\u751f\u7269\u5b66\u91cd\u590d\u548c\u6280\u672f\u6027\u91cd\u590d\u878d\u5408\u540e\uff0c\u518d\u8fdb\u884c\u8ba1\u7b97\u7edf\u8ba1\u3002\r\n\r\n--pool-tech-reps<\/span>\r\n    \u5c06\u6280\u672f\u6027\u91cd\u590d\u8fdb\u884c\u878d\u5408\u540e\uff0c\u5728\u8fdb\u884c\u8ba1\u7b97\u7edf\u8ba1\u3002\r\n\r\n--test<\/span>\r\n    \u641c\u7d22Myrna\u9700\u8981\u7684\u5de5\u5177(Bowtie, R\/Bioconductor \u548c fastq-dump\uff09\uff0c\u6765\u68c0\u6d4b\r\nMyrna\u80fd\u5426\u6b63\u786e\u8fd0\u884c\u3002\r\n\r\n--tmpdir `<int>`  default: \/tmp\/Myrna\/invoke.scripts<\/span>\r\n    \u4e34\u65f6\u6587\u4ef6\u5b58\u653e\u7684\u4f4d\u7f6e\uff0c\u662f\u4e00\u4e2a\u52a8\u6001\u751f\u6210\u7684\u811a\u672c\u3002<\/pre>\n
\u56db. \u4e2a\u4eba\u611f\u53d7<\/h1>\n
\u4f7f\u7528\u65f6\uff0c\u751f\u6210\u7684\u7ed3\u679c\u6ca1\u6709rpkm\u503c\uff0cp-value\u503c\u53ca\u9884\u671f\u7684\u56fe\u8868\u7ed3\u679c\u3002\u4e0d\u77e5\u5230\u54ea\u513f\u51fa\u9519\u4e86\u3002\u6bd4\u5bf9\u7684\u4e4b\u524d\u7684\u8fc7\u7a0b\u90fd\u662f\u6b63\u5e38\u7684\u3002\u540c\u65f6\u4f7f\u7528sra\u6587\u4ef6\u65f6\u5019\uff0c\u63d0\u793afastq-dump\u627e\u4e0d\u5230\u6216\u65e0\u6cd5\u6267\u884c(\u5b9e\u9645\u4e0a\u5728–test\u7684\u65f6\u5019\u53ef\u884c)\u3002\u65e0\u6cd5\u6b63\u5e38\u4f7f\u7528myrna\u3002\u8d39\u5fc3\u8d39\u529b\uff0c\u4e0d\u60f3\u6df1\u7a76\u4e86…\u60b2\u5267…\u518d\u53bb\u7814\u7a76cufflinks\u53bb\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
Myrna\u7684\u4e3b\u8981\u7528\u9014\u662f\u4f7f\u7528RNA-seq\u6570\u636e\u6765\u8ba1\u7b97\u57fa\u56e0\u5dee\u5f02\u8868\u8fbe\u3002\u672c\u6587\u8be6\u7ec6\u4ecb\u7ecd\u4e86\u5176\u4f7f\u7528\u53c2\u6570\u3002\u53ef\u60dc\u7684\u662f\u4f5c\u8005\u4e0d\u80fd\u6b63\u5e38\u4f7f\u7528\u8be5\u8f6f\u4ef6\uff0c\u539f\u56e0\u672a\u77e5\u3002 \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[43],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/866"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=866"}],"version-history":[{"count":38,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/866\/revisions"}],"predecessor-version":[{"id":868,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/866\/revisions\/868"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=866"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=866"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=866"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}