{"id":660,"date":"2021-10-18T12:10:41","date_gmt":"2021-10-18T03:10:41","guid":{"rendered":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/?p=660"},"modified":"2021-10-18T12:11:17","modified_gmt":"2021-10-18T03:11:17","slug":"post-660","status":"publish","type":"post","link":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/archives\/660","title":{"rendered":"Trinity\u3067cDNA\u3092\u30a2\u30bb\u30f3\u30d6\u30eb"},"content":{"rendered":"<p>Trinity\u306fRNA-Seq\u306e\u30ea\u30fc\u30c9\u3092\u30a2\u30bb\u30f3\u30d6\u30eb\u3057\u3066\u3001cDNA\u306e\u914d\u5217\u3092\u3064\u304f\u308a\u307e\u3059\u3002<\/p>\n<h4>\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9<\/h4>\n<p>Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038\/nbt.1883. PubMed PMID: 21572440.<\/p>\n<h3>\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n<p>docker\u3092\u4f7f\u3063\u3066\u74b0\u5883\u3092\u3064\u304f\u308a\u307e\u3059\u3002docker search trinity\u3068\u3057\u3066\u307f\u308b\u3068 docker.io\/trinityrnaseq\/trinityrnaseq (\u4ee5\u4e0btrinityrnaseq)\u304c\u898b\u3064\u304b\u308a\u307e\u3057\u305f\u3002\u3053\u308c\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002<\/p>\n<pre class=\"console\"># docker pull docker.io\/trinityrnaseq\/trinityrnaseq\n# docker inspect docker.io\/trinityrnaseq\/trinityrnaseq\n        \"Config\": {\n            (\u9014\u4e2d\u7701\u7565)\n            \"Cmd\": [\n                \"\/bin\/bash\"\n            ],\n            (\u9014\u4e2d\u7701\u7565)\n            \"WorkingDir\": \"\/usr\/local\/src\",\n<\/pre>\n<p>\u4e2d\u8eab\u3092docker inspect \u3067\u8abf\u3079\u3066\u307f\u308b\u3068\u3001WorkingDir\u304c\/user\/local\/src\u3067\u3001Cmd\u304c\/bin\/bash\u3068\u306a\u3063\u3066\u3044\u308b\u3053\u3068\u304c\u308f\u304b\u308a\u307e\u3059\u3002docker run\u3067\u8d77\u52d5\u3059\u308b\u3068\/bin\/bash\u304c\u52d5\u304f\u3053\u3068\u304c\u308f\u304b\u308a\u307e\u3059\u3002-d\u3092\u3064\u3051\u3066\u3044\u308c\u3070attach\u3067\u63a5\u7d9a\u3057\u307e\u3059\u3002exec\u3067-d\u3092\u3064\u3051\u308b\u3068\u30d0\u30c3\u30af\u30b0\u30e9\u30a6\u30f3\u30c9\u3067\u5b9f\u884c\u3057\u307e\u3059\u3002<\/p>\n<h3>\u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306e\u8a2d\u5b9a<\/h3>\n<p>docker\u5185\u306etrinity\u3092\u5b9f\u884c\u3059\u308b\u3068\u304d\u306b\u554f\u984c\u306b\u306a\u308b\u306e\u304c\u3001fastq\u30d5\u30a1\u30a4\u30eb\u306e\u7f6e\u304d\u5834\u6240\u3068trinity\u306e\u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306e\u30d1\u30fc\u30df\u30c3\u30b7\u30e7\u30f3\u3067\u3059\u3002\u3053\u308c\u3089\u3092\u30b3\u30f3\u30c6\u30ca\u5185\u306e\u30d5\u30a1\u30a4\u30eb\u3068\u3057\u3066\u7528\u610f\u3059\u308b\u5834\u5408\u306fdocker cp\u3067\u30d5\u30a1\u30a4\u30eb\u3092\u79fb\u52d5\u3059\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002\u30b3\u30f3\u30c6\u30ca\u306e\u5916\u306b\u4f5c\u3063\u305f\u30d5\u30a1\u30a4\u30eb\u3092\u30de\u30a6\u30f3\u30c8\u3059\u308b\u5834\u5408\u306f\u3001\u6240\u6709\u6a29\u306b\u6ce8\u610f\u3059\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059(docker\u5185\u3067\u306froot\u3068\u3057\u3066\u3075\u308b\u307e\u3046)\u3002<\/p>\n<table>\n<thead>\n<tr>\n<td><\/td>\n<td>\u524d\u51e6\u7406<\/td>\n<td>\u5f8c\u51e6\u7406<\/td>\n<td>\u30c7\u30e1\u30ea\u30c3\u30c8<\/td>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>\u30d5\u30a1\u30a4\u30eb\u3092\u30b3\u30d4\u30fc\u3059\u308b\u5834\u5408<\/td>\n<td>\n<pre class=\"console\"># docker cp fastq_files trinity:\/tmp<\/pre>\n<\/td>\n<td>\n<pre class=\"console\"># docker cp trinity:\/tmp\/ .\/<\/pre>\n<\/td>\n<td>\u30d5\u30a1\u30a4\u30eb\u306e\u30b3\u30d4\u30fc\u306b\u6642\u9593\u304c\u304b\u304b\u308b\u3002<\/td>\n<\/tr>\n<tr>\n<td rowspan=\"2\">\u30de\u30a6\u30f3\u30c8\u3059\u308b\u5834\u5408<\/td>\n<td>\n<pre class=\"console\"># mkdir working_dir\n# chmod 777 working_dir<\/pre>\n<\/td>\n<td>\n<pre class=\"console\"># chown user. -R working_dir<\/pre>\n<\/td>\n<td>\u30d5\u30a1\u30a4\u30eb\u306e\u30d1\u30fc\u30df\u30c3\u30b7\u30e7\u30f3\u306b\u60a9\u307e\u3055\u308c\u308b\u3002<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>fastq\u30d5\u30a1\u30a4\u30eb\u306e\u6307\u5b9a<\/h3>\n<p>\u901a\u5e38\u6b21\u4e16\u4ee3\u578b\u30b7\u30fc\u30b1\u30f3\u30b5\u30fc\u306f\u4e00\u3064\u306e\u30b5\u30f3\u30d7\u30eb\u3092\u8907\u6570\u306e\u30d5\u30a1\u30a4\u30eb\u306b\u5206\u3051\u3066\u51fa\u529b\u3057\u307e\u3059\u3002\u6700\u8fd1\u306etrinity\u3067\u306f\u3053\u308c\u3089\u3092\u4e00\u89a7\u3059\u308b\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210\u3057\u3001\u305d\u308c\u3092&#8211;sample_files\u30aa\u30d7\u30b7\u30e7\u30f3\u3068\u3057\u3066\u6307\u5b9a\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002\u7d50\u69cb\u306a\u6570\u304c\u3042\u308b\u3068\u9762\u5012\u306a\u306e\u3067\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u3064\u304f\u308a\u307e\u3057\u305f\u3002<\/p>\n<pre class=\"console\"># ls Nco_Roots_*\nNco_Roots_S8_L001_R1_001.fastq.gz\nNco_Roots_S8_L001_R2_001.fastq.gz\nNco_Roots_S8_L002_R1_001.fastq.gz\nNco_Roots_S8_L002_R2_001.fastq.gz\nNco_Roots_S8_L003_R1_001.fastq.gz\nNco_Roots_S8_L003_R2_001.fastq.gz\nNco_Roots_S8_L004_R1_001.fastq.gz\nNco_Roots_S8_L004_R2_001.fastq.gz\n# ls *_R2_*.fastq.gz | sed -e \"s\/_S[0-9]\\+.*\/\/\" &gt;sample\n# ls *_R2_*.fastq.gz &gt;R2\n# paste sample sample &lt;(sed s\/_R2_\/_R1_\/ R2) R2 &gt;samples_file.txt\n<\/pre>\n<p><!--\n# ls *_R1_*.fastq.gz | sed -ne \"s\/_[0-9]_S[0-9]\\+.*\/\/p\" &gt;sample\n# ls *_R1_*.fastq.gz | sed -ne \"s\/\\(_[0-9]\\)_S[0-9]\\+.*\/\\1\/p\" &gt;rep\n# ls *_R1_*.fastq.gz | sed -ne \"\/_[0-9]_S[0-9]\\+.*\/p\" &gt;R1\n# paste sample rep R1 &gt;&gt;samples_file.txt--><\/p>\n<h3>docker\u30b3\u30f3\u30c6\u30ca\u306e\u4f5c\u6210<\/h3>\n<p>-d\u3067\u30d0\u30c3\u30af\u30b0\u30e9\u30a6\u30f3\u30c9\u5b9f\u884c(\u30b3\u30f3\u30c6\u30ca\u304c\u5e38\u6642Up\u306e\u72b6\u614b)\u3001-i\u3067<\/p>\n<pre class=\"console\"># docker run -dit --volume \/path\/to\/working_dir:\/home --workdir \/home --name trinity docker.io\/trinityrnaseq\/trinityrnaseq\n<\/pre>\n<h3>trinity\u306e\u5b9f\u884c<\/h3>\n<p>docker exec\u306b-d\u30aa\u30d7\u30b7\u30e7\u30f3\u3092\u3064\u3051\u308b\u3068\u30d0\u30c3\u30af\u30b0\u30e9\u30a6\u30f3\u30c9\u5b9f\u884c\u3068\u306a\u308a\u307e\u3059\u3002<\/p>\n<pre class=\"console\"># docker exec -d trinity Trinity --seqType fa --max_memory 64G --samples_file samples_file.txt\n<\/pre>\n<h3>\u7d50\u5c40\u306e\u3068\u3053\u308d<\/h3>\n<p>fastq\u30d5\u30a1\u30a4\u30eb\u306e\u6307\u5b9a\u306fsamples_file\u3067\u306f\u3046\u307e\u304f\u3044\u304b\u306a\u304b\u3063\u305f\u306e\u3067\u3001\u30aa\u30fc\u30bd\u30c9\u30c3\u30af\u30b9\u306bleft.fq\u3068right.fq\u3092\u7528\u610f\u3057\u307e\u3057\u305f\u3002<\/p>\n<pre class=\"console\"># zcat *_R1_*.fastq.gz &gt;left.fq\n# zcat *_R2_*.fastq.gz &gt;right.fq\n# docker exec -d trinity Trinity --seqType fa --max_memory 64G --left left.fq --right right.fq\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Trinity\u306fRNA-Seq\u306e\u30ea\u30fc\u30c9\u3092\u30a2\u30bb\u30f3\u30d6\u30eb\u3057\u3066\u3001cDNA\u306e\u914d\u5217\u3092\u3064\u304f\u308a\u307e\u3059\u3002 \u30ea\u30d5\u30a1\u30ec\u30f3\u30b9 Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[17],"tags":[21,19,20],"_links":{"self":[{"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/posts\/660"}],"collection":[{"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/comments?post=660"}],"version-history":[{"count":16,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/posts\/660\/revisions"}],"predecessor-version":[{"id":676,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/posts\/660\/revisions\/676"}],"wp:attachment":[{"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/media?parent=660"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/categories?post=660"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/tags?post=660"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}