{"id":1926,"date":"2022-06-30T20:19:26","date_gmt":"2022-06-30T11:19:26","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1926"},"modified":"2022-06-30T20:19:26","modified_gmt":"2022-06-30T11:19:26","slug":"bioinfofinder%e3%82%92%e4%bd%bf%e3%81%a3%e3%81%a6%e6%96%b0%e8%a6%8f%e3%82%b2%e3%83%8e%e3%83%a0%e3%81%ab%e3%82%a2%e3%83%8e%e3%83%86%e3%83%bc%e3%82%b7%e3%83%a7%e3%83%b3%e3%82%92%e4%bb%98%e3%81%91","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1926","title":{"rendered":"[bioinfo]Finder\u3092\u4f7f\u3063\u3066\u65b0\u898f\u30b2\u30ce\u30e0\u306b\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u3092\u4ed8\u3051\u308b"},"content":{"rendered":"\n

\u6700\u8fd1\u767a\u8868\u3055\u308c\u305fFinder (Banerjee et al., 2021)\u3092\u4f7f\u3046\u3002<\/p>\n\n\n\n

Finder\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u306f\u57fa\u672c\u7684\u306bgit\u306b\u3042\u308b\u8aac\u660e\u306e\u3068\u304a\u308a\u306b\u884c\u3046\u306e\u3060\u304c\u3001\u8aac\u660e\u4e0d\u8db3\u3084\u9593\u9055\u3044\u304c\u3042\u308b\u306e\u3067\u6ce8\u610f\u304c\u5fc5\u8981\u3067\u3042\u308b\u3002<\/p>\n\n\n\n

git\u304b\u3089\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3001\u30d1\u30b9\u3092\u901a\u3059<\/p>\n\n\n\n

git clone https:\/\/github.com\/sagnikbanerjee15\/Finder.git\ncd Finder\necho \"export PATH=\\$PATH:$(pwd)\" >> ~\/.bashrc\nsource ~\/.bashrc<\/pre>\n\n\n\n
Braker2\u306e\u5b9f\u884c\u306b\u5fc5\u8981\u306aGeneMark-ET\u3068\u305d\u306e\u30e9\u30a4\u30bb\u30f3\u30b9\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3059\u308b\u3002
http:\/\/topaz.gatech.edu\/GeneMark\/license_download.cgi\u3092\u30d6\u30e9\u30a6\u30b6\u3067\u958b\u3044\u3066\u3001\u4e0a\u304b\u3089\u4e8c\u6bb5\u76ee\u306b\u3042\u308b”GeneMark-ES\/ET\/EP ver 4.62_lic<\/strong>“\u3001”LINUX 64<\/strong>“\u3092\u9078\u629e\u3057\u3001\u5fc5\u8981\u306a\u60c5\u5831\u3092\u8a18\u5165\u3057\u305f\u4e0a\u3067\u3001”I agree to the terms of this license agreement”\u306e\u30dc\u30bf\u30f3\u3092\u62bc\u3059\u3002
\u30d7\u30ed\u30b0\u30e9\u30e0\u672c\u4f53\u306e\u30ea\u30f3\u30af\u3068\u30e9\u30a4\u30bb\u30f3\u30b9\u306e\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u7528\u30ea\u30f3\u30af\u304c\u73fe\u308c\u308b\u306e\u3067\u3001\u3069\u3061\u3089\u3082\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u3001Finder\u306e\u30d5\u30a9\u30eb\u30c0\u306e\u76f4\u4e0b\u306b\u5c55\u958b\u3059\u308b\uff08git\u306b\u306fwget\u5f8c\u306b\u30b3\u30de\u30f3\u30c9\u3067\u5c55\u958b\u3059\u308b\u3088\u3046\u306b\u306a\u3063\u3066\u3044\u308b\u304c\u3001\u305d\u308c\u3060\u3068\u500b\u5225\u306e\u30d5\u30a9\u30eb\u30c0\u304c\u3067\u304d\u3066\u30b9\u30af\u30ea\u30d7\u30c8\u304c\u8d70\u3089\u306a\u3044\uff09\u3002<\/strong><\/p>\n\n\n\n
Finder\u3067\u4f7f\u3046RNAseq\u306e\u60c5\u5831\u3092metadata.csv\u306e\u30d5\u30a1\u30a4\u30eb\u306b\u66f8\u304d\u8fbc\u3080\u3002\u6ce8\u610f\u70b9\u3068\u3057\u3066\u3001\u30d5\u30a1\u30a4\u30eb\u540d\u306b\u5927\u6587\u5b57\u3092\u542b\u3081\u306a\u3044\u3001\u62e1\u5f35\u5b50\u3092fastq\u306b\u3059\u308b\u3001\u30d5\u30a1\u30a4\u30eb\u306e\u7f6e\u304d\u5834\u3068\u3057\u3066\u30d7\u30ed\u30b0\u30e9\u30e0\u304b\u3089\u30a2\u30af\u30bb\u30b9\u3067\u304d\u308b\u5834\u6240\u306b\u3059\u308b\u306a\u3069\u304c\u3042\u308b\u3002<\/p>\n\n\n\n
Column Name<\/th>Column Description<\/th>Mandatory<\/th><\/tr><\/thead>
BioProject<\/td>\u30d7\u30ed\u30b8\u30a7\u30af\u30c8\u540d\u3002De Novo\u30b2\u30ce\u30e0\u306e\u5834\u5408\u306f\u30c0\u30df\u30fc\u306e\u30d7\u30ed\u30b8\u30a7\u30af\u30c8\u540d\u306b\u3059\u308b\u3002<\/td>YES<\/strong><\/td><\/tr>
SRA Accession<\/td>SRA\u30a2\u30af\u30bb\u30b7\u30e7\u30f3\u3060\u304c\u3001De Novo\u30b2\u30ce\u30e0\u306e\u5834\u5408\u306fRNAseq\u306e\u30d5\u30a1\u30a4\u30eb\u540d\u306b\u3059\u308b\u3002\u30da\u30a2\u30a8\u30f3\u30c9\u30c7\u30fc\u30bf\u306e\u5834\u5408\u3001\u4f8b\u3048\u3070”data_1.fastq”\u3001”data_2.fastq”\u3068\u3044\u3046\u30d5\u30a1\u30a4\u30eb\u540d\u306e\u5834\u5408\u306f\u3001”data”\u3067OK\uff08foward\u3068revese\u306e\u30d5\u30a1\u30a4\u30eb\u540d\u306e\u6700\u5f8c\u306f”_1″\u3068”_2″\u3002\u30d5\u30a1\u30a4\u30eb\u540d\u306e\u62e1\u5f35\u5b50\u306ffastq\u306b\u3059\u308b\u3002<\/td>YES<\/strong><\/td><\/tr>
Tissues<\/td>RNAseq\u30c7\u30fc\u30bf\u306e\u7531\u6765\u306b\u3064\u3044\u3066\u8a18\u8ff0\u3001\u7d44\u7e54\u3084\u30b3\u30f3\u30c7\u30a3\u30b7\u30e7\u30f3\u3092\u8a18\u8ff0\u3057\u3066\u304a\u3051\u3070\u7d44\u7e54\u3054\u3068\u306e\u30ab\u30a6\u30f3\u30c8\u30c7\u30fc\u30bf\u3082\u53d6\u5f97\u3057\u3066\u304f\u308c\u308b\u3002<\/td>YES<\/strong><\/td><\/tr>
Description<\/td>\u30c7\u30fc\u30bf\u306b\u3064\u3044\u3066\u306e\u8a18\u8ff0\u3002finder\u3067\u306f\u4f7f\u308f\u306a\u3044\u3002<\/td>NO<\/td><\/tr>
Date<\/td>RNAseq\u30c7\u30fc\u30bf\u306e\u53d6\u5f97\u65e5\u3002finder\u3067\u306f\u4f7f\u308f\u306a\u3044\u3002<\/td>NO<\/td><\/tr>
Read Length (bp)<\/td>\u30ea\u30fc\u30c9\u9577\u306e\u60c5\u5831\u3002finder\u3067\u306f\u4f7f\u308f\u306a\u3044\u3002<\/td>NO<\/td><\/tr>
Ended<\/td>PE\u304bSE\u3092\u8a18\u8ff0\u3002<\/td>YES<\/strong><\/td><\/tr>
RNA-Seq<\/td>\u3068\u308a\u3042\u3048\u305a1\u3068\u8a18\u8ff0<\/td>YES<\/strong><\/td><\/tr>
process<\/td>\u3068\u308a\u3042\u3048\u305a1\u3068\u8a18\u8ff0\u30020\u3092\u5165\u529b\u3059\u308b\u3068\u305d\u306e\u30d5\u30a1\u30a4\u30eb\u306f\u7121\u8996\u3055\u308c\u308b\u3002<\/td>YES<\/strong><\/td><\/tr>
Location<\/td>RNAseq\u306e\u30d5\u30a1\u30a4\u30eb\u304c\u683c\u7d0d\u3055\u308c\u3066\u3044\u308b\u30d5\u30a9\u30eb\u30c0\u306e\u7d76\u5bfe\u30d1\u30b9\u3092\u5165\u529b\u3002<\/td>YES<\/strong><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n
finder\u3092\u5b9f\u884c\u3059\u308b\u3002CPU 56\u30b3\u30a2\u30011TB RAM\u306e\u30de\u30b7\u30f3\u3092\u7a3c\u50cd\u3055\u305b\u3066\u5b8c\u4e86\u307e\u3067\u4e00\u6669\u306f\u304b\u304b\u308b\u3002<\/p>\n\n\n\n
run_finder -mf {metadata.csv\u306e\u7d76\u5bfe\u30d1\u30b9} -n {cpu\u6570} -out_dir {output\u30d5\u30a9\u30eb\u30c0\u306e\u7d76\u5bfe\u30d1\u30b9} -g {\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u30b2\u30ce\u30e0\u30d5\u30a1\u30a4\u30eb\u306e\u7d76\u5bfe\u30d1\u30b9} -gm {genemaker\u306e\u7d76\u5bfe\u30d1\u30b9} -gml {genemaker\u306e\u30e9\u30a4\u30bb\u30f3\u30b9\u306e\u7d76\u5bfe\u30d1\u30b9} -om VERT -fm singularity 1>run.out 2>run.error<\/pre>\n","protected":false},"excerpt":{"rendered":"
\u6700\u8fd1\u767a\u8868\u3055\u308c\u305fFinder (Baner<\/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=1926","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1926","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\/1926","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=1926"}],"version-history":[{"count":2,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1926\/revisions"}],"predecessor-version":[{"id":1929,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1926\/revisions\/1929"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1926"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1926"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1926"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}