{"id":30229,"date":"2024-02-28T18:13:31","date_gmt":"2024-02-28T10:13:31","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30229"},"modified":"2024-02-28T18:13:32","modified_gmt":"2024-02-28T10:13:32","slug":"%e6%96%b0%e6%89%8b%e4%b8%8a%e8%b7%af%ef%bc%8c%e7%bb%88%e4%ba%8e%e8%b7%91%e9%80%9a%e4%ba%86%ef%bc%9a%e5%88%a9%e7%94%a8edta%e6%b3%a8%e9%87%8a%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%9a%84%e9%87%8d%e5%a4%8d","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30229","title":{"rendered":"\u65b0\u624b\u4e0a\u8def\uff0c\u7ec8\u4e8e\u8dd1\u901a\u4e86\uff1a\u5229\u7528edta\u6ce8\u91ca\u57fa\u56e0\u7ec4\u7684\u91cd\u590d\u5e8f\u5217\uff08\u4ee5\u62df\u5357\u82a5\u4e3a\u4f8b\uff09"},"content":{"rendered":"

\u65b0\u624b\u4e0a\u8def\uff0c\u7ec8\u4e8e\u8dd1\u901a\u4e86\uff1a\u5229\u7528edta\u6ce8\u91ca\u57fa\u56e0\u7ec4\u7684\u91cd\u590d\u5e8f\u5217\uff08\u4ee5\u62df\u5357\u82a5\u4e3a\u4f8b\uff09<\/p>\n

\u8fd8\u8bb0\u5f97\u5c0f\u679c\u4e4b\u524d\u5206\u4eab\u4e86\u5728Ubuntu\u7cfb\u7edf\u4e2d\u5b89\u88c5miniconda\u53caedta\u5417\uff0c\u73b0\u5728\u7ec8\u4e8e\u53ef\u4ee5\u5f00\u59cb\u6ce8\u91ca\u4e86\uff0c\u5c0f\u679c\u6df1\u523b\u9610\u91ca\u4e86\u60f3\u5403\u732a\u8089\u4ece\u517b\u732a\u5f00\u59cb\u8fd9\u4e00\u884c\u4e3a\uff01<\/p>\n

\u5f53\u5929\u771f\u7684\u5c0f\u679c\u4ee5\u4e3a\u88c5\u597d\u8f6f\u4ef6\u5bf9\u4ee3\u7801\u590d\u5236\u7c98\u8d34\uff08\u4e0d\u662f\uff09\u5c31\u53ef\u4ee5\u8f7b\u677e\u6ce8\u91ca\u65f6\uff0c\u60b2\u5267\u5c31\u8bde\u751f\u4e86\uff01\u56e0\u4e3a\u4f5c\u4e3a\u4e00\u53ea\u83dc\u679c\uff0c\u5979\u8fd8\u4e0d\u660e\u767derro\uff01erro\uff01error\uff01\u662f\u80fd\u628a\u4eba\u903c\u75af\u7684\u3002<\/p>\n

\u5e9f\u8bdd\u4e0d\u591a\u8bf4\uff0c\u6211\u4eec\u8fd8\u662f\u8fdb\u5165\u6b63\u9898\u5427\uff01\u4e0a\u671f\u8bf4\u8981\u7528\u5230\u5c0f\u9f20\u57fa\u56e0\u7ec4\uff0c\u4f46\u662f\u8981\u7ec3\u4e60\u7684\u8bdd\u8fd8\u662f\u9009\u62e9\u57fa\u56e0\u7ec4\u6bd4\u8f83\u5c0f\u7684\u7269\u79cd\u66f4\u5feb\uff0c\u6240\u4ee5\u5c0f\u679c\u6362\u6210\u4e86\u62df\u5357\u82a5\u3002<\/p>\n

1. \u4e0b\u8f7d\u57fa\u56e0\u7ec4\u6570\u636e\u5e76\u89e3\u538b\u7f29Arabidopsis thaliana genome assembly TAIR10.1 – NCBI – NLM (nih.gov)<\/a><\/p>\n

<\/p>\n

\u5728ncbi\u63d0\u4f9b\u4e863\u79cd\u65b9\u5f0f\uff0cdownload\u53ef\u4ee5\u76f4\u63a5\u4e0b\u8f7d\u5230\u672c\u5730\uff0cdatasets\u5219\u8981\u4e0b\u8f7dncbi datasets\u8fdb\u884c\u5b89\u88c5\uff0ccurl\u5219\u9700\u8981\u5df2\u5b89\u88c5curl\uff0c\u6bd4\u5982\u8bf4\u7528curl\u5b89\u88c5\u5219\u76f4\u63a5\u590d\u5236\u547d\u4ee4\u5230\u7ec8\u7aef\u5c31\u53ef\u4ee5\u4e86\u3002<\/p>\n

<\/p>\n

\u5728\u8fc7\u7a0b\u4e2d\u9700\u8981\u7528\u5230genometools\uff0c\u6211\u4eec\u7528miniconda\u5b89\u88c5\u5373\u53ef\uff0c\u4e0d\u6307\u5b9a\u5b89\u88c5\u76ee\u5f55\u4f1a\u9ed8\u8ba4\u5b89\u88c5\u5230conda\u73af\u5883\u4e0b\u7684pkgs\u76ee\u5f55\u4e0b\u3002<\/p>\n

conda install -c bioconda genometools-genometools<\/p>\n

\u67e5\u770b\u5b89\u88c5\u60c5\u51b5<\/p>\n

conda list genometools<\/p>\n

4. \u5f00\u59cb\u6ce8\u91ca\uff01<\/p>\n

conda activate EDTA<\/p>\n

nohup perl ~\/EDTA\/EDTA.pl \\<\/p>\n

–genome ~\/my_folder\/GCF_000001735.4\/GCF_000001735.4_TAIR10.1_genomic.fna \\<\/p>\n

–species others \\<\/p>\n

–step all \\<\/p>\n

–overwrite 1 \\<\/p>\n

–cds ~\/my_folder\/GCF_000001735.4\/cds_from_genomic.fna \\<\/p>\n

–sensitive 1 \\<\/p>\n

–anno 1 \\<\/p>\n

–evaluate 1 \\<\/p>\n

–force 1 \\<\/p>\n

–u 1.3e-8 \\<\/p>\n

–threads 4 \\<\/p>\n

–debug 0 \\<\/p>\n

>output.log &<\/p>\n

\u4e3a\u4e86\u66f4\u597d\u7406\u89e3\uff0c\u5c0f\u679c\u5c06\u4ee3\u7801\u7684\u542b\u4e49\u653e\u5728\u4e0b\u9762\uff1a<\/p>\n

\u8bb0\u5f97\u5148\u6fc0\u6d3bEDTA\u73af\u5883\u54e6\uff01<\/p>\n

nohup: \u5ffd\u7565SIGHUP\u4fe1\u53f7\uff0c\u5373\u4f7f\u5f53\u524d\u7ec8\u7aef\u5173\u95ed\u4e5f\u80fd\u7ee7\u7eed\u8fd0\u884c\u3002<\/p>\n

–genome\uff1a\u6307\u5b9a\u5f85\u5206\u6790\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u6587\u4ef6\u8def\u5f84<\/p>\n

–species\uff1a\u6307\u5b9a\u5f85\u5206\u6790\u57fa\u56e0\u7ec4\u7684\u7269\u79cd\u4fe1\u606f\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201cothers\u201d<\/p>\n

–step\uff1a\u6307\u5b9a\u5206\u6790\u6b65\u9aa4\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201call\u201d\u8868\u793a\u6267\u884c\u5b8c\u6574\u7684\u5206\u6790\u6d41\u7a0b<\/p>\n

–overwrite\uff1a\u5982\u679c\u8f93\u51fa\u6587\u4ef6\u5df2\u7ecf\u5b58\u5728\uff0c\u662f\u5426\u8986\u76d6\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201c1\u201d\u8868\u793a\u8986\u76d6<\/p>\n

–cds\uff1a\u6307\u5b9a\u5305\u542bCDS\u5e8f\u5217\u7684\u6587\u4ef6\u8def\u5f84\uff0c\u8fd9\u4e2a\u6587\u4ef6\u901a\u5e38\u7531\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6\u63d0\u4f9b<\/p>\n

–sensitive\uff1a\u662f\u5426\u4f7f\u7528\u8f83\u4e3a\u654f\u611f\u7684TE\u8bc6\u522b\u7b97\u6cd5\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201c1\u201d\u8868\u793a\u4f7f\u7528<\/p>\n

–anno\uff1a\u662f\u5426\u4f7f\u7528\u5df2\u6709\u7684\u57fa\u56e0\u7ec4\u6ce8\u91ca\u4fe1\u606f\u8fdb\u884c\u5206\u6790\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201c1\u201d\u8868\u793a\u4f7f\u7528<\/p>\n

–evaluate\uff1a\u662f\u5426\u5bf9\u5206\u6790\u7ed3\u679c\u8fdb\u884c\u8bc4\u4f30\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201c1\u201d\u8868\u793a\u4f7f\u7528<\/p>\n

–force\uff1a\u662f\u5426\u5f3a\u5236\u6267\u884c\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201c1\u201d\u8868\u793a\u5f3a\u5236\u6267\u884c<\/p>\n

–u\uff1a\u6307\u5b9aTE\u5e93\u4e2d\u7684\u6700\u5c0f\u4e0d\u540c\u79cd\u540c\u65cf\u91cd\u590d\u5143\u4ef6\u6570\u91cf\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201c1.3e-8\u201d<\/p>\n

–threads\uff1a\u6307\u5b9a\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\u91cf\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201c4\u201d<\/p>\n

–debug\uff1a\u662f\u5426\u8f93\u51fa\u8c03\u8bd5\u4fe1\u606f\uff0c\u8fd9\u91cc\u6307\u5b9a\u4e3a\u201c0\u201d\u8868\u793a\u4e0d\u8f93\u51fa<\/p>\n

edta.log\uff1a\u5c06\u6807\u51c6\u8f93\u51fa\u91cd\u5b9a\u5411\u5230\u540d\u4e3a\u201cedta.log\u201d\u7684\u6587\u4ef6\u4e2d<\/p>\n

&\uff1a\u5c06\u8fdb\u7a0b\u653e\u5230\u540e\u53f0\u8fd0\u884c\u3002<\/p>\n

<\/p>\n

\u63a5\u4e0b\u6765\u53ef\u4ee5\u901a\u8fc7\u67e5\u770b\u8f93\u51fa\u65e5\u5fd7\u6765\u67e5\u770b\u8fdb\u5ea6<\/p>\n

cat output.log<\/p>\n

<\/p>\n

\u53ef\u4ee5\u770b\u5230\u5c0f\u679c\u7684\u8fdb\u5ea6\u76ee\u524d\u662f\u6ca1\u6709erro\u7684~<\/p>\n

\u5c0f\u679c\u5728\u8fd9\u4e00\u8fc7\u7a0b\u4e2d\u72af\u4e86\u4e00\u4e9b\u9519\u8bef\uff0c\u7ed9\u5927\u5bb6\u501f\u9274\uff1a<\/p>\n

1.\u5fd8\u8bb0\u6fc0\u6d3bEDTA \u73af\u5883\u5bfc\u81f4\u62a5\u9519<\/p>\n

2.\u6ca1\u6709\u5b89\u88c5genometools<\/p>\n

3.\u8def\u5f84\u9519\u8bef<\/p>\n

\u5f53\u7136\u4e86\uff0c\u6bcf\u4e2a\u4eba\u9047\u5230\u7684\u95ee\u9898\u53ef\u80fd\u4e0d\u4e00\u6837\uff0c\u5728\u8fc7\u7a0b\u4e2d\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u62a5\u9519\u6765\u89e3\u51b3\u95ee\u9898\u3002<\/p>\n

\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 \u00a0– \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/a><\/p>\n

\u5982\u679c\u60f3\u7528\u670d\u52a1\u5668\u53ef\u4ee5\u8054\u7cfb\u5fae\u4fe1\uff1a18502195490\uff08\u5904\u7406\u5927\u91cf\u6570\u636e\u7684\u65f6\u5019\u4e0d\u7528\u670d\u52a1\u5668\u7528\u4ec0\u4e48\uff01\u5feb\u6765\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u5427\uff01\uff09<\/p>\n","protected":false},"excerpt":{"rendered":"

\u65b0\u624b\u4e0a\u8def\uff0c\u7ec8\u4e8e\u8dd1\u901a\u4e86\uff1a\u5229\u7528edta\u6ce8\u91ca\u57fa\u56e0\u7ec4\u7684\u91cd\u590d\u5e8f\u5217\uff08\u4ee5\u62df\u5357\u82a5\u4e3a\u4f8b\uff09 \u8fd8\u8bb0\u5f97\u5c0f\u679c\u4e4b\u524d\u5206\u4eab\u4e86\u5728Ubuntu\u7cfb\u7edf […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30229"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=30229"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30229\/revisions"}],"predecessor-version":[{"id":30234,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30229\/revisions\/30234"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30229"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=30229"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=30229"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}