{"id":1487,"date":"2021-04-04T00:36:50","date_gmt":"2021-04-03T15:36:50","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1487"},"modified":"2023-12-21T23:11:01","modified_gmt":"2023-12-21T14:11:01","slug":"bioinfosra%e3%83%87%e3%83%bc%e3%82%bf%e3%82%92%e5%8a%b9%e7%8e%87%e7%9a%84%e3%81%ab%e3%83%80%e3%82%a6%e3%83%b3%e3%83%ad%e3%83%bc%e3%83%89%e3%81%99%e3%82%8b%e3%80%82","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1487","title":{"rendered":"[bioinfo]SRA\u30c7\u30fc\u30bf\u3092\u52b9\u7387\u7684\u306b\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3059\u308b\u3002"},"content":{"rendered":"\n<div class=\"wp-block-group is-layout-flow wp-block-group-is-layout-flow\">\n<p style=\"font-size:15px\">SRR\u306e\u30ea\u30b9\u30c8\u3092\u4f5c\u308a\u3001parallel\u306b\u30d1\u30a4\u30d7\u3067\u6e21\u3057\u3066sratoolkit\u306eprefetch\u3092\u4e26\u5217\u51e6\u7406\u3067\u30e9\u30f3\u3002<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\" style=\"font-size:15px\">sort -u srr_list | parallel -j 4 \"prefetch --max-size 30g {}\"<\/pre>\n\n\n\n<p style=\"font-size:15px\">\u305d\u306e\u3042\u3068pfastq-dump\u3067fastq.gz\u306b\u5909\u63db<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\" style=\"font-size:15px\">parallel-fastq-dump --threads 8 *.sra --gzip --split-files<\/pre>\n\n\n\n<p style=\"font-size:15px\">\u5f8c\u304b\u3089\u601d\u3063\u305f\u304c\u3001\u4e0b\u8a18\u306e\u30b3\u30de\u30f3\u30c9\u3067\u6700\u521d\u304b\u3089gzip\u3068\u3057\u3066\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u304f\u308c\u3070\u3088\u304b\u3063\u305f\u306e\u304b\u3082\u3057\u308c\u306a\u3044\u3002<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\" style=\"font-size:15px\">sort -u srr_list | parallel -j 4 \"fastq-dump --gzip --split-files {}\"<\/pre>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>SRR\u306e\u30ea\u30b9\u30c8\u3092\u4f5c\u308a\u3001parallel\u306b<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"colormag_page_container_layout":"default_layout","colormag_page_sidebar_layout":"default_layout","_locale":"ja","_original_post":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1487","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1487","post","type-post","status-publish","format-standard","hentry","category-protocol","ja"],"_links":{"self":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1487","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1487"}],"version-history":[{"count":3,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1487\/revisions"}],"predecessor-version":[{"id":2522,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1487\/revisions\/2522"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1487"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1487"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1487"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}