{"id":1673,"date":"2021-12-21T12:22:49","date_gmt":"2021-12-21T03:22:49","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1673"},"modified":"2021-12-21T13:17:41","modified_gmt":"2021-12-21T04:17:41","slug":"bioinfo-fosmid-%e4%bd%8d%e7%bd%ae%e3%82%92%e3%82%b2%e3%83%8e%e3%83%a0%e3%83%96%e3%83%a9%e3%82%a6%e3%82%b6%ef%bc%88jbrowse2%ef%bc%89%e3%81%ab%e5%ae%9f%e8%a3%85%e3%81%99%e3%82%8b","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1673","title":{"rendered":"[bioinfo] fosmid \u4f4d\u7f6e\u3092\u30b2\u30ce\u30e0\u30d6\u30e9\u30a6\u30b6\uff08jbrowse2\uff09\u306b\u5b9f\u88c5\u3059\u308b"},"content":{"rendered":"<p>\u5927\u91cf\u30c7\u30fc\u30bf\u306e\u6642\u4ee3\u304c\u6765\u3066\u3082\u5b9f\u9a13\u751f\u7269\u5b66\u306b\u304a\u3051\u308b\u3001\u30b2\u30ce\u30e0\u30e9\u30a4\u30d6\u30e9\u30ea\u306e\u91cd\u8981\u6027\u306f\u5909\u308f\u3089\u306a\u3044\u3002fosmid\u30e9\u30a4\u30d6\u30e9\u30ea\u306f\u907a\u4f1d\u5b50\u30ec\u30d9\u30eb\u306e\u89e3\u6790\u306b\u306f\u91cd\u5b9d\u3059\u308b\u30b5\u30a4\u30ba\u306e\u30b2\u30ce\u30e0\u30e9\u30a4\u30d6\u30e9\u30ea\u306a\u306e\u3060\u304c\u3001fosmid-end\u306e\u30b7\u30fc\u30af\u30a8\u30f3\u30b9\u60c5\u5831\u306e\u307f\u306a\u306e\u3067\u3001\u30b2\u30ce\u30e0\u4e0a\u306e\u6b32\u3057\u3044\u4f4d\u7f6e\u306e\u30af\u30ed\u30fc\u30f3\u304c\u5206\u304b\u308b\u3088\u3046\u306b\u3057\u3066\u307b\u3057\u3044\u3068\u3044\u3046\u30ea\u30af\u30a8\u30b9\u30c8\u3092\u53d7\u3051\u3066\u3001\u30b2\u30ce\u30e0\u30e9\u30a4\u30d6\u30e9\u30ea\u306b\u5b9f\u88c5\u3057\u3066\u307f\u305f\u3002<\/p>\n<p>fosmid-end sequence\u3092RepeatMasker\u3067\u51e6\u7406\u3002RepeatMasker\u306fconda\u3067\u5c0e\u5165\u3002<\/p>\n\n\n<pre class=\"wp-block-code\"><code>conda create -n repeatmasker python=3.7\nconda activate repeatmasker\nconda install -c bioconda repeatmasker\nRepeatMasker -e hmmer -pa 48 fosmid-end.fasta<\/code><\/pre>\n\n\n\n<p>\u51e6\u7406\u3057\u305ffosmid-end sequence\u306e\u60c5\u5831\u3092\u30af\u30a8\u30ea\u3068\u3057\u3066\u30b2\u30ce\u30e0\u4e0a\u3067\u691c\u7d22\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>blastn -query fosmid-end.fasta.masked -db genome.fa -max_target_seq 1 -num_threads 48  -outfmt 7 -out fosmid-end.fasta.masked.blastn.out<\/code><\/pre>\n\n\n\n<p>besthit\u306e\u30c7\u30fc\u30bf\u3060\u3051\u306b\u3057\u305f\u3044\u306e\u3067\u3001\u6b21\u306e\u30ef\u30f3\u30e9\u30a4\u30ca\u30fc\u3067\u51e6\u7406\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>cat fosmid-end.fasta.masked.blastn.out | awk '\/hits found\/{getline;print}' | grep -v \"#\" > fosmid-end.fasta.masked.blastn.out.besthit.txt<\/code><\/pre>\n\n\n\n<p>gff\u306b\u5909\u63db\u3059\u308b\u3002\u3044\u308d\u3044\u308d\u5de5\u592b\u3059\u308b\u5fc5\u8981\u304c\u3042\u308b\u306e\u3067\u3001\u30a8\u30af\u30bb\u30eb\u3067\u884c\u3063\u305f\u3002\u3082\u3057\u304b\u3057\u305f\u3089blast2gff\u306a\u308b\u30b9\u30af\u30ea\u30d7\u30c8\u304c\u3044\u308d\u3044\u308d\u8ee2\u304c\u3063\u3066\u3044\u308b\u306e\u3067\u305d\u308c\u3089\u3092\u4f7f\u3048\u3070\u826f\u3044\u306e\u304b\u3082\u3057\u308c\u306a\u3044\u3002\u57fa\u672c\u7684\u306agff3\u306e\u30ab\u30e9\u30e0\u306f\u4ee5\u4e0b\u3002<\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>seqid: \u67d3\u8272\u4f53\u306e\u4f4d\u7f6e\u306a\u3069<\/li><li>source: \u30e9\u30a4\u30d6\u30e9\u30ea\u3084\u30d7\u30ed\u30b8\u30a7\u30af\u30c8\u306e\u60c5\u5831<\/li><li>type: &#8220;mRNA&#8221;\u3001&#8221;exon&#8221;\u306a\u3069\u306efeature\u60c5\u5831<\/li><li>start: \u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u306e\u958b\u59cb\u4f4d\u7f6e<\/li><li>end: \u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u306e\u7d42\u4e86\u4f4d\u7f6e<\/li><li>score: \u4fe1\u983c\u5ea6\u306a\u3069\u306e\u6570\u5024<\/li><li>strand: \u914d\u5217\u306e\u5411\u304d<\/li><li>phase: \u30b3\u30c9\u30f3\u306e\u958b\u59cb\u4f4d\u7f6e<\/li><li>attributes: ID\u3001Name\u3001Parent\u306a\u3069\u306e\u60c5\u5831\u3002\u5b9f\u306f\u3053\u3053\u304c\u4e00\u756a\u91cd\u8981 <\/li><\/ol>\n\n\n\n<p>\u4f5c\u88fd\u3057\u305fgff\u30d5\u30a1\u30a4\u30eb\u3092\u30bd\u30fc\u30c8\u3057\u3001gzip\u5727\u7e2e\u3001tabix\u51e6\u7406\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>gt gff3 -sourtlines -tidy -retainids fosmid.gff > fosmid.sorted.gff\nbgzip fosmid.sorted.gff\ntabix fosmid.sorted.gff.gz<\/code><\/pre>\n\n\n\n<p>jbrowse2\u306b\u5b9f\u88c5\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>jbrowse add-track fosmid.sorted.gff.gz --out usr\/bin\/jbrowse2 --name fosmid_library --assemblyNames genome --load copy<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u5927\u91cf\u30c7\u30fc\u30bf\u306e\u6642\u4ee3\u304c\u6765\u3066\u3082\u5b9f\u9a13\u751f\u7269\u5b66\u306b\u304a\u3051<\/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=1673","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1673","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\/1673","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=1673"}],"version-history":[{"count":3,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1673\/revisions"}],"predecessor-version":[{"id":1677,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1673\/revisions\/1677"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1673"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1673"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1673"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}