{"id":1948,"date":"2013-10-14T14:58:52","date_gmt":"2013-10-14T06:58:52","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=1948"},"modified":"2014-01-03T11:19:27","modified_gmt":"2014-01-03T03:19:27","slug":"%e4%bd%bf%e7%94%a8trimmonmatic%e8%bf%9b%e8%a1%8cngs-reads%e7%9a%84%e8%bf%87%e6%bb%a4%e4%b8%8e%e4%bf%ae%e5%89%aa","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1948","title":{"rendered":"\u4f7f\u7528Trimmonmatic\u8fdb\u884cNGS reads\u7684\u8fc7\u6ee4\u4e0e\u4fee\u526a"},"content":{"rendered":"<h1>1. Trimmomatic<\/h1>\n<p>Trimmomatic\u4f7f\u7528JAVA\u8fd0\u884c\uff0c\u901f\u5ea6\u5feb\u3002\u540c\u65f6\u8be5\u8f6f\u4ef6\u8fdb\u884creads QC\u7684\u539f\u7406\u975e\u5e38\u597d\u3002\u56e0\u6b64\uff0c\u6700\u63a8\u8350\u4f7f\u7528\u6b64\u8f6f\u4ef6\u8fdb\u884cNGS reads\u7684QC\u3002<br \/>\n\u53c2\u8003\u6587\u732e\uff1a<a href=\"http:\/\/nar.oxfordjournals.org\/content\/40\/W1\/W622.long\" target=\"_blank\">Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7.<\/a><\/p>\n<h1>2. \u5e38\u7528\u4f8b\u5b50<\/h1>\n<pre>java -jar \/opt\/biosoft\/Trimmomatic-0.30\/trimmomatic-0.30.jar PE \\\r\n-threads 20 -phred33 reads1.fastq reads2.fastq \\\r\nreads1.clean.fastq reads1.unpaired.fastq reads2.clean.fastq reads2.unpaired.fastq \\\r\nILLUMINACLIP:\/opt\/biosoft\/Trimmomatic-0.30\/adapters\/TruSeq3-PE.fa:2:30:10 \\\r\nLEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50<\/pre>\n<h1>3. \u4f7f\u7528\u53c2\u6570<\/h1>\n<p>\u6709\u5173\u8be5\u8f6f\u4ef6\u7684\u8be6\u7ec6\u4f7f\u7528\u65b9\u6cd5\uff0c\u89c1\uff1a <a href=\"http:\/\/www.usadellab.org\/cms\/index.php?page=trimmomatic\" target=\"_blank\">Trimmomatic: A flexible read trimming tool for Illumina NGS data<\/a><\/p>\n<pre><span style=\"color: #ff00ff;\">PE\/SE<\/span>\r\n    \u8bbe\u5b9a\u5bf9Paired-End\u6216Single-End\u7684reads\u8fdb\u884c\u5904\u7406\uff0c\u5176\u8f93\u5165\u548c\u8f93\u51fa\u53c2\u6570\u7a0d\u6709\u4e0d\u4e00\u6837\u3002\r\n<span style=\"color: #ff00ff;\">-threads<\/span>\r\n    \u8bbe\u7f6e\u591a\u7ebf\u7a0b\u8fd0\u884c\u6570\r\n<span style=\"color: #ff00ff;\">-phred33<\/span>\r\n    \u8bbe\u7f6e\u78b1\u57fa\u7684\u8d28\u91cf\u683c\u5f0f\uff0c\u53ef\u9009pred64\r\n<span style=\"color: #ff00ff;\">ILLUMINACLIP:TruSeq3-PE.fa:2:30:10<\/span>\r\n    \u5207\u9664adapter\u5e8f\u5217\u3002\u53c2\u6570\u540e\u9762\u5206\u522b\u63a5adapter\u5e8f\u5217\u7684fasta\u6587\u4ef6\uff1a\u5141\u8bb8\u7684\u6700\u5927mismatch\r\n\u6570\uff1apalindrome\u6a21\u5f0f\u4e0b\u5339\u914d\u78b1\u57fa\u6570\u9608\u503c\uff1asimple\u6a21\u5f0f\u4e0b\u7684\u5339\u914d\u78b1\u57fa\u6570\u9608\u503c\u3002\r\n<span style=\"color: #ff00ff;\">LEADING:3<\/span>\r\n    \u5207\u9664\u9996\u7aef\u78b1\u57fa\u8d28\u91cf\u5c0f\u4e8e3\u7684\u78b1\u57fa\r\n<span style=\"color: #ff00ff;\">TRAILING:3<\/span>\r\n    \u5207\u9664\u5c3e\u7aef\u78b1\u57fa\u8d28\u91cf\u5c0f\u4e8e3\u7684\u78b1\u57fa\r\n<span style=\"color: #ff00ff;\">SLIDINGWINDOW:4:15<\/span>\r\n    \u4ece5'\u7aef\u5f00\u59cb\u8fdb\u884c\u6ed1\u52a8\uff0c\u5f53\u6ed1\u52a8\u4f4d\u70b9\u5468\u56f4\u4e00\u6bb5\u5e8f\u5217(window)\u7684\u5e73\u5747\u78b1\u57fa\u4f4e\u4e8e\u9608\u503c\uff0c\u5219\u4ece\u8be5\u5904\u8fdb\u884c\u5207\u9664\u3002Windows\u7684size\u662f4\u4e2a\u78b1\u57fa\uff0c\u5176\u5e73\u5747\u78b1\u57fa\r\n\u8d28\u91cf\u5c0f\u4e8e15\uff0c\u5219\u5207\u9664\u3002\r\n<span style=\"color: #ff00ff;\">MINLEN:50<\/span>\r\n    \u6700\u5c0f\u7684reads\u957f\u5ea6\r\nCROP:&lt;length&gt;\r\n    \u4fdd\u7559reads\u5230\u6307\u5b9a\u7684\u957f\u5ea6\r\nHEADCROP:&lt;length&gt;\r\n    \u5728reads\u7684\u9996\u7aef\u5207\u9664\u6307\u5b9a\u7684\u957f\u5ea6\r\nTOPHRED33\r\n    \u5c06\u78b1\u57fa\u8d28\u91cf\u8f6c\u6362\u4e3apred33\u683c\u5f0f\r\nTOPHRED64\r\n    \u5c06\u78b1\u57fa\u8d28\u91cf\u8f6c\u6362\u4e3apred64\u683c\u5f0f<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. Trimmomatic Trimmomatic\u4f7f\u7528JAVA\u8fd0\u884c\uff0c\u901f\u5ea6\u5feb\u3002\u540c &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=1948\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/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":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1948"}],"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=1948"}],"version-history":[{"count":12,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1948\/revisions"}],"predecessor-version":[{"id":2074,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1948\/revisions\/2074"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1948"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1948"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1948"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}