{"id":1890,"date":"2022-06-01T00:36:43","date_gmt":"2022-05-31T15:36:43","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1890"},"modified":"2022-06-01T00:38:20","modified_gmt":"2022-05-31T15:38:20","slug":"bioinfop_rna_scaffolder%e3%82%92%e4%bd%bf%e3%81%a3%e3%81%a6scaffold%e9%95%b7%e3%82%92%e6%94%b9%e5%96%84%e3%81%99%e3%82%8b","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1890","title":{"rendered":"[bioinfo]P_RNA_Scaffolder\u3092\u4f7f\u3063\u3066Scaffold\u9577\u3092\u6539\u5584\u3059\u308b"},"content":{"rendered":"\n<p><a href=\"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-018-4567-3\">Zhu et al., P_RNA_Scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads (2018) <em>BMC Genomics<\/em><\/a><\/p>\n\n\n\n<p>https:\/\/github.com\/CAFS-bioinformatics\/P_RNA_scaffolder<br>\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3002blat\u7b49\u306e\u5b9f\u884c\u6a29\u9650\u304c\u4ed8\u3044\u3066\u3044\u306a\u3044\u306e\u3067\u4ed8\u52a0\u3059\u308b\u3002\u307e\u305f\u3001RNAseq\u306e\u30c7\u30fc\u30bf\u306f\u8907\u6570\u3042\u308b\u5834\u5408\u304c\u591a\u3044\u306e\u3067\u3001\u3042\u3089\u304b\u3058\u3081cat\u3057\u3066\u304a\u304f\u3002<\/p>\n\n\n\n<p>hisat2\u3067RNAseq\u306e\u30c7\u30fc\u30bf\u3092\u3059\u3067\u306b\u30a2\u30bb\u30f3\u30d6\u30eb\u3057\u3066\u3042\u308b\u30b2\u30ce\u30e0\u30c7\u30fc\u30bf\u306b\u30de\u30c3\u30d4\u30f3\u30b0<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>#\u521d\u671f\u30b2\u30ce\u30e0\u30c7\u30fc\u30bf\u306b\u3064\u3044\u3066\u306ehisat2\u306e\u30a4\u30f3\u30c7\u30c3\u30af\u30b9\u3092\u69cb\u7bc9\nhisat2-build genome.fa genome\n#\u30de\u30c3\u30d4\u30f3\u30b0\nhisat2 -x genome -1 concat_rnaseq_1.fq -2 concat_rnaseq_2.fq -k3 -p32 --pen-noncansplice 1000000 -S input.sam<\/code><\/pre>\n\n\n\n<p>P_RNA_scaffolder\u3092\u5b9f\u884c\u3002Ubuntu\u306e\u5834\u5408\u306b\u306fsh\u3067\u306f\u306a\u304fbash\u3067\u306a\u3044\u3068\u30a8\u30e9\u304c\u2015\u51fa\u308b\u3002\u307e\u305f\u3001\u30d7\u30ec\u30b3\u30f3\u30d1\u30a4\u30eb\u3055\u308c\u3066\u3044\u308bC\u3067\u66f8\u304b\u308c\u305f\u30d7\u30ed\u30b0\u30e9\u30e0\u306f\u4e0a\u8a18\u306e\u3068\u304a\u308a\u3001\u5b9f\u884c\u6a29\u9650\u3092\u4e0e\u3048\u3066\u304a\u304f\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>bash \/path_to_P_RNA_scaffoder\/P_RNA_scaffolder.sh -d \/path_to_P_RNA_scaffoder -i input.sam -j genome.fa -f concat_rnaseq_1.fq -r concat_rnaseq_2.fq -o out -t 32<\/code><\/pre>\n\n\n\n<p>\u3000\u6570\u6642\u9593\u3067\u5b8c\u4e86\u3059\u308b\u3002\u5287\u7684\u306b\u6539\u5584\u3059\u308b\u3068\u3044\u3046\u307b\u3069\u3067\u306f\u306a\u3044\u304c\u3001scaffold N50=1Mb\u306e\u30b2\u30ce\u30e0\u306b\u5bfe\u3057\u3066\u3001100Gb\u7a0b\u5ea6\u306eRNAseq\u30c7\u30fc\u30bf\u3092\u4f7f\u3063\u305f\u5834\u5408\u3001N50=1.2Mb\u7a0b\u5ea6\u306b\u4f38\u3073\u308b\u3002\u307e\u305f\u3001\u907a\u4f1d\u5b50\u5168\u9577\u3082\u3042\u308b\u7a0b\u5ea6\u88dc\u5b8c\u3067\u304d\u308b\u3088\u3046\u306b\u306a\u308b\u3088\u3046\u3067\u3042\u308b\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Zhu et al., P_RNA_Sc<\/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=1890","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1890","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\/1890","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=1890"}],"version-history":[{"count":4,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1890\/revisions"}],"predecessor-version":[{"id":1896,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1890\/revisions\/1896"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1890"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1890"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1890"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}