{"id":27290,"date":"2024-01-31T17:01:51","date_gmt":"2024-01-31T09:01:51","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27290"},"modified":"2024-01-31T17:01:52","modified_gmt":"2024-01-31T09:01:52","slug":"sratools%ef%bc%9a%e4%b8%80%e7%ab%99%e5%bc%8f%e8%a7%a3%e5%86%b3-sra-%e6%95%b0%e6%8d%ae%e4%b8%8b%e8%bd%bd%e3%80%81%e8%bd%ac%e6%8d%a2%e5%92%8c%e5%88%86%e6%9e%90%e9%97%ae%e9%a2%98","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27290","title":{"rendered":"sratools\uff1a\u4e00\u7ad9\u5f0f\u89e3\u51b3 SRA \u6570\u636e\u4e0b\u8f7d\u3001\u8f6c\u6362\u548c\u5206\u6790\u95ee\u9898"},"content":{"rendered":"<p>\u5927\u5bb6\u597d\uff0c\u6211\u662f\u5c0f\u679c\uff0c\u4eca\u5929\u6211\u8981\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u8d85\u7ea7\u597d\u7528\u7684\u751f\u4fe1\u5c0f\u5de5\u5177\uff0c\u53eb\u505asratools\u3002sratools\u662f\u4ec0\u4e48\u5462\uff1f\u5b83\u662f\u4e00\u4e2a\u53ef\u4ee5\u5e2e\u52a9\u4f60\u4e0b\u8f7d\u3001\u8f6c\u6362\u3001\u5206\u6790NCBI SRA\u6570\u636e\u5e93\u4e2d\u7684\u6d4b\u5e8f\u6570\u636e\u7684\u8f6f\u4ef6\u5305\u3002\u4f60\u53ef\u80fd\u4f1a\u95ee\uff0c\u4e3a\u4ec0\u4e48\u8981\u7528sratools\u5462\uff1f\u6709\u4ec0\u4e48\u597d\u5904\u5462\uff1f\u8ba9\u6211\u6765\u544a\u8bc9\u4f60\u5427\uff01<\/p>\n<p>1. \u4e0b\u8f7d\u5b89\u88c5\u7b80\u5355<\/p>\n<p>\u4e0b\u8f7d\u7f51\u5740\uff1b<a href=\"https:\/\/github.com\/ncbi\/sra-tools.git\">https:\/\/github.com\/ncbi\/sra-tools.git<\/a><\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"517\" class=\"wp-image-27291\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-1.png?resize=640%2C517\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-1.png?w=872 872w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-1.png?resize=300%2C243 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-1.png?resize=768%2C621 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-1.png?resize=600%2C485 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u6216\u8005<a href=\"https:\/\/github.com\/ncbi\/sra-tools\/wiki\/01.-Downloading-SRA-Toolkit\">https:\/\/github.com\/ncbi\/sra-tools\/wiki\/01.-Downloading-SRA-Toolkit<\/a> \u9009\u62e9\u9002\u5408\u81ea\u5df1\u7684\u7248\u672c\u4e0b\u8f7d\u5373\u53ef\u3002<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"490\" class=\"wp-image-27292\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-2.png?resize=640%2C490\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-2.png?w=921 921w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-2.png?resize=300%2C230 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-2.png?resize=768%2C588 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-2.png?resize=600%2C459 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>2. \u4f7f\u7528\u5c31\u66f4\u7b80\u5355\u3002<\/p>\n<p>\u7b2c\u4e00\u6b65\u89e3\u538b\uff1a<\/p>\n<p>$ tar -xzf sratoolkit.3.0.6-ubuntu64.tar.gz<\/p>\n<p>$ cd sratoolkit.3.0.6-ubuntu64\/bin\/<\/p>\n<p>Sratoolkit\u7684\u529f\u80fd\u4e3b\u8981\u6709\u4e0b\u8f7dSRA\u6570\u636e\u3001\u8f6c\u6362\u4e3afastq\u6587\u4ef6\u548c\u67e5\u770bSRA\u6587\u4ef6\u4fe1\u606f\u7b49\u3002<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"159\" class=\"wp-image-27293\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-3.png?resize=640%2C159\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-3.png?w=1532 1532w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-3.png?resize=300%2C74 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-3.png?resize=1024%2C254 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-3.png?resize=768%2C190 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-3.png?resize=600%2C149 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-3.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>sratools\u53ef\u4ee5\u8ba9\u4f60\u5feb\u901f\u5730\u4e0b\u8f7dSRA\u6570\u636e\uff0c\u4e0d\u7528\u62c5\u5fc3\u7f51\u7edc\u4e0d\u7a33\u5b9a\u6216\u8005\u6587\u4ef6\u635f\u574f\u7684\u95ee\u9898\u3002\u4f60\u53ea\u9700\u8981\u8f93\u5165SRA\u7684accession number\uff0c\u5c31\u53ef\u4ee5\u4e00\u952e\u4e0b\u8f7d\u4f60\u60f3\u8981\u7684\u6570\u636e\u662f\u4e0d\u662f\u5f88\u65b9\u4fbf\u5462\uff1f\u6bd4\u5982\uff0c\u4f60\u60f3\u4e0b\u8f7d\u4e00\u4e2a\u5173\u4e8e\u690d\u7269\u53f6\u7eff\u4f53\u7684\u9879\u76ee\uff0c\u5c31\u53ea\u9700\u8981\u8f93\u5165\u547d\u4ee4\uff1a<\/p>\n<p>$ .\/prefetch SRR24757234<\/p>\n<p>\u8fd9\u4e2a\u6587\u4ef6\u6709\u70b9\u5927\uff0c\u8981\u8010\u5fc3\u7b49\u51e0\u5206\u949f\uff0c\u7136\u540e\u6211\u4eec\u5c31\u5f97\u5230\u4e86\u4e00\u4e2aSRR24757234\/\u7684\u6587\u4ef6\u5939\uff0c,\u6587\u4ef6\u5939\u5185\u6709\u4e00\u4e2aSRR24757234.sra\u6587\u4ef6\uff0c\u5b83\u5c31\u662f\u6211\u4eec\u7684\u6a21\u677f\u6587\u4ef6\u5566\u3002<\/p>\n<p>\u901a\u5e38\u60c5\u51b5\u4e0b\uff0c\u6211\u4eec\u9700\u8981\u7528\u7684sratools\u683c\u5f0f\u8f6c\u6362\u529f\u80fd\uff0c\u5c06SRA\u6570\u636e\u8f6c\u6362\u4e3a\u5e38\u89c1\u7684FASTQ\u683c\u5f0f\u3002\u53ea\u9700\u8981\u8f93\u5165\u547d\u4ee4\uff1a<\/p>\n<p>$ .\/fastq-dump SRR24757234<\/p>\n<p>\u5f97\u5230\u6587\u4ef6SRR24757234.fastq\uff0c\u5c31\u53ef\u4ee5\u628aSRR24757234\u8fd9\u4e2a\u6837\u672c\u7684SRA\u6587\u4ef6\u8f6c\u6362\u4e3aFASTQ\u6587\u4ef6\u4e86\u3002<\/p>\n<p>\u6211\u4eec\u4e5f\u53ef\u4ee5\u6dfb\u52a0\u4e00\u4e9b\u53c2\u6570\u6765\u8c03\u6574\u8f93\u51fa\u7684\u683c\u5f0f\uff0c\u6bd4\u5982\uff1a<\/p>\n<p>$ .\/fastq-dump &#8211;split-files &#8211;gzip SRR24757234<\/p>\n<p>\u5f97\u5230SRR24757234_1.fastq.gz\u548cSRR24757234_2.fastq.gz\u4e24\u4e2a\u6587\u4ef6\uff0c\u8fd9\u6837\u5c31\u53ef\u4ee5\u628aSRR1552456\u8fd9\u4e2a\u6837\u672c\u7684\u53cc\u7aef\u6d4b\u5e8f\u6570\u636e\u5206\u522b\u8f93\u51fa\u4e3a\u4e24\u4e2a\u538b\u7f29\u7684FASTQ\u6587\u4ef6\u4e86\u3002\u53ea\u4e0d\u8fc7\u4f1a\u6bd4\u8f83\u6162\uff0c\u53ef\u4ee5\u540e\u53f0\u8fd0\u884c\u3002<\/p>\n<p>sratools\u7684\u53e6\u4e00\u4e2a\u5e38\u7528\u7684\u529f\u80fd\u662f\u67e5\u770bSRA\u6570\u636e\u3002\u4f7f\u7528sra-stat\u547d\u4ee4\u53ef\u4ee5\u67e5\u770bSRA\u6570\u636e\u7684\u7edf\u8ba1\u4fe1\u606f\uff0c\u5305\u62ec\u78b1\u57fa\u6570\u3001\u8bfb\u957f\u3001\u8d28\u91cf\u5206\u5e03\u7b49\u3002\u4f8b\u5982\uff0c\u8981\u67e5\u770bSRR390728\u8fd9\u4e2a\u6837\u672c\u7684SRA\u6570\u636e\u7684\u78b1\u57fa\u6570\u548c\u8bfb\u957f\u5206\u5e03\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n<p>$ .\/sra-stat -x &#8211;statistics SRR24757234 &gt; SRR24757234.xml<\/p>\n<p>-x\u8868\u793a\u4ee5xml\u683c\u5f0f\u8f93\u51fa\uff0c\u8fd9\u6837\u6211\u4eec\u5c31\u5f97\u5230\u4e86\u4e00\u4e2a\u5305\u542b\u6837\u672cSRR24757234\u7684\u7edf\u8ba1\u4fe1\u606f\u6587\u4ef6SRR24757234.xml\u3002<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"482\" height=\"386\" class=\"wp-image-27294\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-4.png?resize=482%2C386\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-4.png?w=482 482w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-4.png?resize=300%2C240 300w\" sizes=\"(max-width: 482px) 100vw, 482px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\uff08\u7f51\u9875\u7684\u90e8\u5206\u5185\u5bb9\uff09<\/p>\n<p>Sratools\u8fd8\u6709\u641c\u7d22\u7279\u5f81\u5e8f\u5217\u7684\u529f\u80fd\u3002\u4f7f\u7528sra-search\u547d\u4ee4\u53ef\u4ee5\u5728SRA\u6570\u636e\u4e2d\u641c\u7d22\u6307\u5b9a\u7684\u5e8f\u5217\u6216\u6a21\u5f0f\uff0c\u652f\u6301\u6b63\u5219\u8868\u8fbe\u5f0f\u3002\u4f8b\u5982\uff0c\u8981\u5728SRR24757234\u8fd9\u4e2a\u6837\u672c\u7684SRA\u6570\u636e\u4e2d\u641c\u7d22\u5305\u542b\u201cATTCGT\u201d\u8fd9\u4e2a\u5e8f\u5217\u7684reads\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n<p>$ .\/sra-search ATTCGT SRR24757234<\/p>\n<p>\u6216\u8005<\/p>\n<p>$ .\/sra-search &#8220;CGTA||ACGT&#8221; -e -a NucStrstr SRR24757234<\/p>\n<p>\u6b64\u4f8b\u5b50\u4e2d&#8221;CGTA||ACGT&#8221;\u8868\u793a\u641c\u7d22\u5305\u542b\u201cCGTA\u201d\u6216\u201cACGT\u201d\u7684\u5e8f\u5217\u3002-e\u9009\u9879\u8868\u793a\u4f7f\u7528\u6269\u5c55\u6b63\u5219\u8868\u8fbe\u5f0f\u8fdb\u884c\u641c\u7d22\u3002-a NucStrstr\u00a0\u9009\u9879\u6307\u5b9a\u4e86\u8981\u4f7f\u7528\u201cNucStrstr\u201d\u7b97\u6cd5\u3002\u8fd9\u6837\u5c31\u53ef\u4ee5\u627e\u5230\u6211\u4eec\u611f\u5174\u8da3\u7684\u7279\u5f81\u5e8f\u5217\u5566\uff01<\/p>\n<p>Sratools\u8fd8\u6709\u9a8c\u8bc1SRA\u6570\u636e\u7684\u529f\u80fd\u3002\u4f7f\u7528vdb-validate\u547d\u4ee4\u53ef\u4ee5\u9a8c\u8bc1SRA\u6570\u636e\u7684\u5b8c\u6574\u6027\u548c\u4e00\u81f4\u6027\uff0c\u68c0\u67e5\u662f\u5426\u6709\u635f\u574f\u6216\u9519\u8bef\u3002\u4f8b\u5982\uff0c\u8981\u9a8c\u8bc1SRR24757234\u8fd9\u4e2a\u6837\u672c\u7684SRA\u6570\u636e\u662f\u5426\u6709\u6548\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n<p>$ .\/vdb-validate SRR24757234<\/p>\n<p>\u5982\u679c\u6587\u4ef6\u5b8c\u6574\uff0c\u4f1a\u5f97\u5230\u201cDatabase &#8216;SRR24757234.sra&#8217; is consistent\u201d\u7684\u7ed3\u679c\u3002<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"167\" class=\"wp-image-27295\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-5.png?resize=640%2C167\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-5.png?w=982 982w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-5.png?resize=300%2C79 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-5.png?resize=768%2C201 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-27290-5.png?resize=600%2C157 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u603b\u4e4b\uff0csratools\u662f\u4e00\u4e2a\u975e\u5e38\u5b9e\u7528\u7684\u751f\u4fe1\u5de5\u5177\uff0c\u5b83\u53ef\u4ee5\u8ba9\u4f60\u66f4\u65b9\u4fbf\u5730\u4e0b\u8f7d\u3001\u8f6c\u6362\u3001\u5206\u6790SRA\u6570\u636e\uff0c\u8282\u7701\u4f60\u7684\u65f6\u95f4\u548c\u7cbe\u529b\u3002\u5982\u679c\u4f60\u8fd8\u6ca1\u6709\u5c1d\u8bd5\u8fc7sratools\uff0c\u90a3\u5c31\u8d76\u5feb\u53bb\u4e0b\u8f7d\u5b89\u88c5\u5427\uff01\u5e0c\u671b\u4f60\u80fd\u559c\u6b22sratools\uff0c\u4e5f\u5e0c\u671b\u4f60\u80fd\u5728\u751f\u4fe1\u7684\u9053\u8def\u4e0a\u8d8a\u8d70\u8d8a\u8fdc\uff01\u8c22\u8c22\u5927\u5bb6\uff01<br \/>\n&#8220;`<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5927\u5bb6\u597d\uff0c\u6211\u662f\u5c0f\u679c\uff0c\u4eca\u5929\u6211\u8981\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u8d85\u7ea7\u597d\u7528\u7684\u751f\u4fe1\u5c0f\u5de5\u5177\uff0c\u53eb\u505asratools\u3002sratools\u662f\u4ec0\u4e48\u5462\uff1f [&hellip;]<\/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\/27290"}],"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=27290"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27290\/revisions"}],"predecessor-version":[{"id":27296,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27290\/revisions\/27296"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=27290"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=27290"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=27290"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}