{"id":1154,"date":"2020-01-07T23:00:48","date_gmt":"2020-01-07T14:00:48","guid":{"rendered":"http:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1154"},"modified":"2020-04-05T23:55:43","modified_gmt":"2020-04-05T14:55:43","slug":"bioinfodnbseq-g400%e3%81%aese%e3%83%87%e3%83%bc%e3%82%bftrimming%e8%a8%ad%e5%ae%9a%ef%bc%88trimmomatic%ef%bc%89","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1154","title":{"rendered":"[bioinfo]DNBSEQ-G400\u306eSE\u30c7\u30fc\u30bftrimming\u8a2d\u5b9a\uff08trimmomatic\uff09"},"content":{"rendered":"\n<p>trimmomatic\u306e\u30b3\u30de\u30f3\u30c9\u3067\u30cf\u30de\u3063\u305f\u306e\u3068\u3001\u521d\u306eDNBSEQ\u4e14\u3064hiseq\u3092\u542b\u3081\u3066single end\u30c7\u30fc\u30bf\u306f\u521d\u3081\u3066\u306a\u306e\u3067\u30e1\u30e2\u3002<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">java -jar trimmomatic-0.39.jar SE -threads 16 -phred33 dnbseq_001.fq ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:30<\/pre>\n\n\n\n<p>trimmomatic\u306eSE\u8a2d\u5b9a\u3067\u3001\u30a2\u30c0\u30d7\u30bf\u30fc\u306f<del>TruSeq3-SE.fa<\/del>BGI\u306e\u8cc7\u6599\u306b\u3042\u3063\u305f\u4e0b\u8a18\u914d\u5217\u3002\u3042\u3068\u306fHiseq\u30c7\u30fc\u30bf\u3068\u307b\u307c\u5909\u308f\u3089\u305a\u3002\u6a19\u6e96\u7684\u306a\u8a2d\u5b9a\u3002<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">Primers for BGISEQ\/DNBSEQ\/MGISEQ library sequencing:\nAll following sequencing primers are included in the sequencing kits of BGISEQ\/DNBSEQ\/MGISEQ system.\n\nRead 1 sequencing primer:\nGCTCACAGAACGACATGGCTACGATCCGACTT\nBarcode SE sequencing primer:\nAAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA\nRead 2 sequencing primer:\nTTGTCTTCCTAAGACCGCTTGGCCTCCGACTT\nBarcode PE sequencing primer:\nATGTCGTTCTGTGAGCCAAGGAGTTG<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted\">The following sequences are used to filter the adapter contamination in raw data.\nForward filter:\nAAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA\nReverse filter:\nAAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>java -jar trimmomati<\/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":"1154","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1154","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\/1154","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=1154"}],"version-history":[{"count":3,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1154\/revisions"}],"predecessor-version":[{"id":1287,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1154\/revisions\/1287"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1154"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1154"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1154"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}