{"id":2124,"date":"2014-06-09T21:42:52","date_gmt":"2014-06-09T13:42:52","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2124"},"modified":"2014-06-09T21:42:52","modified_gmt":"2014-06-09T13:42:52","slug":"%e4%bd%bf%e7%94%a8-l_rna_scaffolder-%e8%bf%9b%e8%a1%8c%e8%bd%ac%e5%bd%95%e7%bb%84%e5%ba%8f%e5%88%97%e5%af%b9%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%ba%8f%e5%88%97%e7%9a%84-rescaffolding","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2124","title":{"rendered":"\u4f7f\u7528 L_RNA_scaffolder \u8fdb\u884c\u8f6c\u5f55\u7ec4\u5e8f\u5217\u5bf9\u57fa\u56e0\u7ec4\u5e8f\u5217\u7684 rescaffolding"},"content":{"rendered":"<h1>1. L_RNA_scaffolder\u7b80\u4ecb<\/h1>\n<p>L_RNA_scaffolder\u80fd\u5229\u7528\u957f\u7684\u8f6c\u5f55\u5b50\u5e8f\u5217\u6765\u8f85\u52a9\u57fa\u56e0\u7ec4\u7684scaffolding\u62fc\u63a5\u3002\u8fd9\u4e9b\u957f\u7684\u8f6c\u5f55\u5b50\u5e8f\u5217\u53ef\u4ee5\u662f454\/sanger\/Ion_Torrent\u7684\u6d4b\u5e8f\u7ed3\u679c\uff0c\u4e5f\u53ef\u4ee5\u662fillumina\u6d4b\u5e8f\u7684de novo\u7ec4\u88c5\u7ed3\u679c\u3002<br \/>\n\u5728\u4f7f\u7528\u6b64\u8f6f\u4ef6\u8fdb\u884cscaffolding\u4e4b\u524d\uff0c\u9700\u8981\u5c06\u8fd9\u4e9b\u957f\u7684\u8f6c\u5f55\u5b50\u5e8f\u5217\u4f7f\u7528BLAT\u8f6f\u4ef6map\u5230\u57fa\u56e0\u7ec4\u4e0a\uff0c\u5f97\u5230PSL\uff08without heading\uff09\u6587\u4ef6\u3002\u5c06\u6b64PSL\u6587\u4ef6\u548c\u57fa\u56e0\u7ec4\u7684\u521d\u6b65\u7ec4\u88c5\u7ed3\u679c\u6587\u4ef6\u8f93\u5165\u5230L_RNA_scaffolder,\u5f88\u5feb\u80fd\u5f97\u5230\u7ed3\u679c\u6587\u4ef6\u3002<\/p>\n<h1>2. L_RNA_scaffolder\u7684\u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/www.fishbrowser.org\/software\/L_RNA_scaffolder\/downloads\/L_RNA_scaffolder.tar.gz\r\n$ tar zxf L_RNA_scaffolder.tar.gz\r\n$ cd L_RNA_scaffolder\r\n\u8fd0\u884c\u8f6f\u4ef6\u7684\u4e3b\u7a0b\u5e8f\uff0c\u4e0d\u52a0\u53c2\u6570\u7ed9\u51fa\u5e2e\u52a9\u4fe1\u606f\r\n$ .\/L_RNA_scaffolder.sh\r\n<\/pre>\n<h1>3. L_RNA_scaffolder\u7684\u4f7f\u7528<\/h1>\n<pre>\r\n\u5148\u4f7f\u7528blat\uff0c\u5c06\u8f6c\u5f55\u5b50\u5e8f\u5217\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\r\n$ blat genome.fasta transcripts.fasta -noHead out.psl\r\n\u518d\u4f7f\u7528L_RNA_scaffolder.sh\u5f97\u5230\u6700\u7ec8\u7684\u57fa\u56e0\u7ec4\u6587\u4ef6\r\n$ mkdir L_RNA_scaffolder_output\r\n$ \/opt\/biosoft\/L_RNA_scaffolder\/L_RNA_scaffolder.sh -d \/opt\/biosoft\/L_RNA_scaffolder\/ -i out.psl -j genome.fasta -o .\/L_RNA_scaffolder_output\r\n\u6700\u7ec8\u7684\u7ed3\u679c\u6587\u4ef6\u4e3a.\/L_RNA_scaffolder_output\/L_RNA_scaffolder.fasta\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. L_RNA_scaffolder\u7b80\u4ecb L_RNA_scaffolder\u80fd\u5229 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2124\">\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":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2124"}],"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=2124"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2124\/revisions"}],"predecessor-version":[{"id":2125,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2124\/revisions\/2125"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2124"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2124"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2124"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}