{"id":599,"date":"2024-10-12T23:39:50","date_gmt":"2024-10-12T15:39:50","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=599"},"modified":"2024-10-18T10:55:39","modified_gmt":"2024-10-18T02:55:39","slug":"%e5%9f%ba%e5%9b%a0%e7%bb%84%e9%87%8d%e5%a4%8d%e5%ba%8f%e5%88%97%e6%b3%a8%e9%87%8a","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2024\/10\/12\/%e5%9f%ba%e5%9b%a0%e7%bb%84%e9%87%8d%e5%a4%8d%e5%ba%8f%e5%88%97%e6%b3%a8%e9%87%8a\/","title":{"rendered":"\u57fa\u56e0\u7ec4\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"599\" class=\"elementor elementor-599\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-efdb2e4 e-flex e-con-boxed e-con e-parent\" data-id=\"efdb2e4\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-533a22c elementor-widget elementor-widget-heading\" data-id=\"533a22c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">\u57fa\u56e0\u7ec4\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f9c4d7e elementor-widget elementor-widget-heading\" data-id=\"f9c4d7e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">\u5f15\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-03e3bfb elementor-widget elementor-widget-text-editor\" data-id=\"03e3bfb\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u76ee\u524d\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\u65b9\u6cd5\u6709\u5f88\u591a\uff0c\u4f46\u662f\u4e3b\u6d41\u76841.EDTA+RepeatMask\uff1b2.Repeatmolder+Repeatmasker\uff0c\u4f46\u662f\u6211\u5728\u4f7f\u7528<span style=\"letter-spacing: -0.1px; color: var( --e-global-color-text ); text-align: var(--text-align); background-color: var(--base-3);\">Repeatmolder+Repeatmasker\u7ec4\u5408\u8fdb\u884c\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\u7684\u65f6\u5019\uff0cUnclass\u7684\u91cd\u590d\u5e8f\u5217\u79cd\u7c7b\u9ad8\u8fbe35%\uff0c\u8fd9\u7ed3\u679c\u663e\u7136\u662f\u6709\u95ee\u9898\u7684\uff0c\u56e0\u6b64\u6211\u53bb\u5bfb\u627e\u539f\u56e0\uff0c\u53d1\u73b0<\/span><span style=\"letter-spacing: -0.1px; color: var( --e-global-color-text ); text-align: var(--text-align); background-color: var(--base-3);\">Repeatmolder\u9884\u6d4b\u7684TE\u5e93\u672c\u8eab\u5c31\u6709\u5f88\u591a\u662fUnclass\uff0c\u6700\u7ec8\u5bfc\u81f4RepeatMasker\u7684\u8f93\u51fa\u7ed3\u679c\u4e5f\u6709\u5f88\u591a\u662fUnclass\u3002\u56e0\u6b64\uff0c\u6211\u91cd\u65b0<\/span><span style=\"background-color: var(--base-3); color: var( --e-global-color-text ); letter-spacing: -0.1px; text-align: var(--text-align);\">\u4f7f\u7528EDTA\u8fdb\u884cTE\u5e93\u7684\u9884\u6d4b\uff0c\u7136\u540e\u4f7f\u7528RepeatMasker\u8fdb\u884c\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\uff0c\u5373<\/span><span style=\"letter-spacing: -0.1px; color: var( --e-global-color-text ); text-align: var(--text-align); background-color: var(--base-3);\">EDTA+RepeatMask\uff0c<\/span><span style=\"background-color: var(--base-3); color: var( --e-global-color-text ); letter-spacing: -0.1px; text-align: var(--text-align);\">\u76ee\u524d\u7ed3\u679c\u8fd8\u6ca1\u8dd1\u51fa\u6765\u3002<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-714a9fb elementor-widget elementor-widget-heading\" data-id=\"714a9fb\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">1. \u8f6f\u4ef6\u5b98\u7f51<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-2cb3f1e elementor-widget elementor-widget-text-editor\" data-id=\"2cb3f1e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><a href=\"https:\/\/github.com\/oushujun\/EDTA\">https:\/\/github.com\/oushujun\/EDTA<\/a><\/p><p>\u00a0<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-555ab05 elementor-widget elementor-widget-heading\" data-id=\"555ab05\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">2. \u4e0b\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-26f0e94 elementor-widget elementor-widget-text-editor\" data-id=\"26f0e94\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u5b98\u7f51\u63a8\u8350\u76f4\u63a5\u7528Conda\u4e0b\u8f7d\uff0c\u4f46\u662f\u6211\u7528Conda\u4e0b\u8f7d\u540e\uff0c\u4f7f\u7528\u7684\u65f6\u5019\u4f1a\u51fa\u73b0LTR\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\u4e0d\u5230\u7684\u95ee\u9898\u3002\u5f53\u6211\u4f7f\u7528\u7b2c\u4e8c\u79cd\u65b9\u6cd5\uff0c\u4e5f\u5c31\u662f\u624b\u52a8\u5b89\u88c5\u4f9d\u8d56\u8f6f\u4ef6\uff0c\u968f\u540e\u4f7f\u7528\uff0c\u5c31\u4e0d\u4f1a\u51fa\u73b0\u8fd9\u4e2a\u95ee\u9898\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a426539 elementor-widget elementor-widget-text-editor\" data-id=\"a426539\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>#Conda \u76f4\u63a5\u5b89\u88c5<\/p><p>conda create -n EDTA<\/p><p>conda activate EDTA<\/p><p>conda install -n bioconda::edta<\/p><p># \u624b\u52a8\u5b89\u88c5\u4f9d\u8d56\uff0c\u7136\u540e\u5b89\u88c5EDTA<\/p><p>mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter<\/p><p>git clone https:\/\/github.com\/oushujun\/EDTA.git<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9bbe09f elementor-widget elementor-widget-heading\" data-id=\"9bbe09f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3. \u8f6f\u4ef6\u4f7f\u7528<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b68ac5a elementor-widget elementor-widget-text-editor\" data-id=\"b68ac5a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u4f7f\u7528\u6d4b\u8bd5\u6570\u636e\u9a8c\u8bc1\u8f6f\u4ef6\u662f\u5426\u4e0b\u8f7d\u6210\u529f\uff0c\u4e00\u822c\u6d4b\u8bd5\u6570\u636e\u96c6\u7684\u8fd0\u884c\u65f6\u95f4\u662f5\u5206\u949f\uff0c\u5982\u679c\u6ca1\u6709\u51fa\u73b0\u9519\u8bef\uff0c\u5219\u8bf4\u660e\u5b89\u88c5\u6ca1\u95ee\u9898\uff08\u8b66\u544a\u6b63\u5e38\uff09\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-73891be elementor-widget elementor-widget-text-editor\" data-id=\"73891be\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p># \u6d4b\u8bd5<\/p>\n<p>perl ..\/EDTA.pl &#8211;genome genome.fa &#8211;cds genome.cds.fa &#8211;curatedlib ..\/database\/rice7.0.0.liban &#8211;exclude genome.exclude.bed &#8211;overwrite 1 &#8211;sensitive 1 &#8211;anno 1 &#8211;threads 10<\/p>\n<p># \u8fd0\u884c\u547d\u4ee4<\/p>\n<p>perl .\/EDTA\/EDTA.pl -genome $Genome -species others -step all -t 30<\/p>\n<p># \u5f53\u4e0d\u6307\u5b9a-anno 1\u65f6\uff0cEDTA\u53ea\u4f1a\u6784\u5efa\u4e00\u4e2aTE\u7684\u5e93\uff0c\u5e76\u4e0d\u4f1a\u8fdb\u884c\u6ce8\u91ca\u3002\u56e0\u6b64\u5f53\u65f6\u60f3\u4e0d\u518d\u4f7f\u7528RepeatMask\u8fdb\u884c\u6ce8\u91ca\uff0c\u800c\u662f\u5b8c\u5168\u7531EDTA\u8fdb\u884c\u5efa\u5e93+\u6ce8\u91ca\uff0c\u53ef\u4ee5\u52a0\u4e0a-anno 1<\/p>\n<p># \u53c2\u6570<\/p>\n<p>&#8211;genome \u57fa\u56e0\u7ec4FASTA\u6587\u4ef6<br>&#8211;species \u6307\u5b9a\u7269\u79cd<br>&#8211;step [all|filter|final|anno] \u6307\u5b9a\u8981\u8fd0\u884cEDTA\u7684\u6b65\u9aa4\u3002all: \u8fd0\u884c\u6574\u4e2a\u6d41\u7a0b\uff08\u9ed8\u8ba4\uff09filter: \u4ece\u539f\u59cbTE\u5f00\u59cb\u5230\u7ed3\u675f\u3002final: \u4ece\u8fc7\u6ee4\u540e\u7684TE\u5f00\u59cb\u5230\u6700\u7ec8\u8fd0\u884c\u3002<br>&#8211;anno [0|1] \u6267\u884c\uff081\uff09\u6216\u4e0d\u6267\u884c\uff080\uff0c\u9ed8\u8ba4\uff09\u5168\u57fa\u56e0\u7ec4TE\u6ce8\u91ca\uff0c\u4f5c\u4e3aTE\u5e93\u6784\u5efa\u540e\u7684\u6b65\u9aa4\u3002<\/p>\n<p># \u8f93\u51fa\u7ed3\u679c<\/p>\n<p>\uff081\uff09\u6784\u5efa\u7684TE\u5e8f\u5217\u5e93\uff0c\u662f\u540e\u9762RepeatMasker\u8fd0\u884c\u7684\u6307\u5b9aTE\u5e93\uff1a&nbsp;$<b>genome.mod.EDTA.TElib.novel.fa<\/b>&nbsp;<\/p>\n<p>\u6ce8\uff1a \u4e0b\u9762\u7684\u7ed3\u679c\u9700\u8981\u6307\u5b9a-<b>anno 1<\/b>\u624d\u80fd\u8f93\u51fa<\/p>\n<p>\uff082\uff09 \u5168\u57fa\u56e0\u7ec4TE\u6ce8\u91ca\uff1a$<b>genome.mod.EDTA.TEanno.gff3<\/b>\u3002\u6b64\u6587\u4ef6\u5305\u542b\u7ed3\u6784\u5b8c\u6574\u548c\u7834\u788e\u7684TE\u6ce8\u91ca\u3002&nbsp;<\/p>\n<p>\uff083\uff09\u5168\u57fa\u56e0\u7ec4TE\u6ce8\u91ca\u6458\u8981\uff1a$<b>genome.mod.EDTA.TEanno.sum<\/b>\u3002&nbsp;<\/p>\n<p>\uff084\uff09\u4f4e\u9608\u503cTE\u63a9\u853d\uff1a$<b>genome.mod.MAKER.masked<\/b>\u3002\u6b64\u6587\u4ef6\u4ec5\u63a9\u853d\u957fTE\uff08\u22651 kb\uff09\u7684\u57fa\u56e0\u7ec4\u6587\u4ef6\u3002\u60a8\u53ef\u4ee5\u5c06\u5176\u7528\u4e8ede novo\u57fa\u56e0\u6ce8\u91ca\u3002\u5728\u5b9e\u8df5\u4e2d\uff0c\u8fd9\u79cd\u65b9\u6cd5\u5c06\u51cf\u5c11\u57fa\u56e0\u533a\u57df\u7684\u8fc7\u5ea6\u63a9\u853d\uff0c\u4ece\u800c\u63d0\u9ad8\u57fa\u56e0\u9884\u6d4b\u8d28\u91cf\u3002\u7136\u800c\uff0c\u521d\u59cb\u57fa\u56e0\u6a21\u578b\u5e94\u5305\u542bTE\uff0c\u5e76\u9700\u8981\u8fdb\u4e00\u6b65\u8fc7\u6ee4\u3002&nbsp;<\/p>\n<p>\uff085\uff09\u7b80\u5355TE\u7684\u6ce8\u91ca\u4e0d\u4e00\u81f4\u6027\uff1a$<b>genome.mod.EDTA.TE.fa.stat.redun.sum<\/b>\u3002&nbsp;<\/p>\n<p>\uff086\uff09\u5d4c\u5957TE\u7684\u6ce8\u91ca\u4e0d\u4e00\u81f4\u6027\uff1a$<b>genome.mod.EDTA.TE.fa.stat.nested.sum<\/b>\u3002&nbsp;<\/p>\n<p>\uff087\uff09\u6574\u4f53\u6ce8\u91ca\u4e0d\u4e00\u81f4\u6027\uff1a$<b>genome.mod.EDTA.TE.fa.stat.all.sum<\/b>\u3002<\/p>\n<p># \u8fd0\u884cRepeatMasker<\/p>\n<p>RepeatMasker -e rmblast -pa 20 -q -lib Lib.fasta genome.fasta -xmall<\/p>\n<p># \u751f\u6210\u8f6f\u5c4f\u853d\u540e\u7684\u5e8f\u5217<\/p>\n<p>maskFile.pl -fasta genome.fasta -annotations genome.out -softmask<\/p>\n<p># \u751f\u6210\u786c\u5c4f\u853d\u540e\u7684\u5e8f\u5217<\/p>\n<p>maskFile.pl -fasta genome.fasta -annotations genome.out<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>\u57fa\u56e0\u7ec4\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca \u5f15\u8a00 \u76ee\u524d\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\u65b9\u6cd5\u6709\u5f88\u591a\uff0c\u4f46\u662f\u4e3b\u6d41\u76841.EDTA+RepeatMask\uff1b2.Re &#8230; <a title=\"\u57fa\u56e0\u7ec4\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2024\/10\/12\/%e5%9f%ba%e5%9b%a0%e7%bb%84%e9%87%8d%e5%a4%8d%e5%ba%8f%e5%88%97%e6%b3%a8%e9%87%8a\/\" aria-label=\"\u9605\u8bfb \u57fa\u56e0\u7ec4\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":610,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-599","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-6"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>\u57fa\u56e0\u7ec4\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"http:\/\/www.majunpeng.com\/index.php\/2024\/10\/12\/\u57fa\u56e0\u7ec4\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\/\" \/>\n<meta property=\"og:locale\" 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