{"id":1923,"date":"2022-06-23T18:58:30","date_gmt":"2022-06-23T09:58:30","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1923"},"modified":"2022-06-23T18:58:34","modified_gmt":"2022-06-23T09:58:34","slug":"bioinforepeatmodeler%e3%81%a7%e3%82%b2%e3%83%8e%e3%83%a0%e4%b8%ad%e3%81%ae%e3%83%aa%e3%83%94%e3%83%bc%e3%83%88%e9%85%8d%e5%88%97%e3%82%92%e5%90%8c%e5%ae%9a%e3%81%97%e3%81%a6repeatmasker%e3%81%a7","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1923","title":{"rendered":"[bioinfo]RepeatModeler\u3067\u30b2\u30ce\u30e0\u4e2d\u306e\u30ea\u30d4\u30fc\u30c8\u914d\u5217\u3092\u540c\u5b9a\u3057\u3066RepeatMasker\u3067\u30de\u30b9\u30af"},"content":{"rendered":"\n<p>RepeatModeler\u3001RepeatMasker\u306fconda\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">conda install -c bioconda repeatmodeler repeatmasker<\/pre>\n\n\n\n<p>\u30b2\u30ce\u30e0\u30c7\u30fc\u30bf\u3092\u691c\u7d22\u7528\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3068\u3057\u3066\u69cb\u7bc9<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">BuildDatabase -name genome_name genome.fasta<\/pre>\n\n\n\n<p>RepeatModer\u3092\u5b9f\u884c\u3059\u308b\u3002blast\u691c\u7d22\u306e\u969b\u306b\u4e00\u3064\u306e\u4e26\u5217\u5b9f\u884c\u306b\u3064\u3044\u30664\u3064\u306ecpu\u3092\u4f7f\u7528\u3059\u308b\u306e\u3067\u3001-pa\u306e\u5024\u306f\u300c\u7dcf\u30b3\u30a2\u6570\u00f74\u300d\u306b\u3057\u3066\u304a\u304f\u300256\u30b3\u30a2\u306e\u5834\u5408\u306f14\u3002<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">RepeatModeler -database genome_name -pa 14<\/pre>\n\n\n\n<p>RepeatMasker\u3092\u5b9f\u884c\u3059\u308b\u3002RepeatMasker\u306ffasta\u30d5\u30a1\u30a4\u30eb\u306eID\u304c50\u6587\u5b57\u3092\u8d8a\u3048\u308b\u3068\u53d7\u3051\u4ed8\u3051\u306a\u3044\u306e\u3067\u3001\u51e6\u7f6e\u3057\u3066\u304a\u304f\u3002\u81ea\u5206\u306e\u5834\u5408\u3001&#8221;:&#8221;\uff08\u30b3\u30ed\u30f3\uff09\u3067\u533a\u5207\u3063\u3066\u305f\u304f\u3055\u3093\u306e\u6587\u5b57\u304c\u5165\u3063\u3066\u3044\u305f\u306e\u3067\u3001\u305d\u308c\u3089\u3092\u524a\u3063\u305f\u3002\u3053\u306e\u3068\u304d\u30d5\u30a1\u30a4\u30eb\u540d\u306b&#8221;+&#8221;\u3092\u4ed8\u3051\u308b\u3068\u3001RepeatMasker\u306eoutput file\u304c\u3059\u3079\u3066\u6d88\u3048\u3066\u3057\u307e\u3046\u306e\u3067\u6ce8\u610f\u3002<br>RepeatMasker\u306e\u30e9\u30a4\u30d6\u30e9\u30ea\u306b\u306fRepeatMasker\u3067\u5f97\u3089\u308c\u305fconsensi.fa\u3092\u4f7f\u3046\u3002<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">sed -e 's\/:.*\/\/' genome.fasta > genome_idfixed.fasta\nRepeatMasker -pa 56 -html -gff -small -lib RepeatModeler_out\/consensi.fa genome_idfixed.fasta -dir RM_out<\/pre>\n\n\n\n<p>-dir\u3067\u6307\u5b9a\u3057\u305f\u30d5\u30a9\u30eb\u30c0\u306b\u7d50\u679c\u304c\u51fa\u3066\u304f\u308b\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>RepeatModeler\u3001Repeat<\/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=1923","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1923","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\/1923","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=1923"}],"version-history":[{"count":1,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1923\/revisions"}],"predecessor-version":[{"id":1924,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1923\/revisions\/1924"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1923"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1923"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1923"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}