{"id":112,"date":"2023-04-25T18:33:29","date_gmt":"2023-04-25T10:33:29","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=112"},"modified":"2023-04-25T18:33:50","modified_gmt":"2023-04-25T10:33:50","slug":"112","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2023\/04\/25\/112\/","title":{"rendered":"Trim Galore \u53bb\u9664\u63a5\u5934+\u8d28\u63a7\u6d41\u7a0b"},"content":{"rendered":"<h1>Trim Galore \u53bb\u9664\u63a5\u5934+\u8d28\u63a7\u6d41\u7a0b<\/h1>\n<h2>\u8f6f\u4ef6\u4f7f\u7528\u7b80\u8981\u8bf4\u660e<\/h2>\n<ul>\n<li>--quality\uff1a\u8bbe\u5b9aPhred quality score\u9608\u503c\uff0c\u9ed8\u8ba4\u4e3a20\u3002<\/li>\n<li>--phred33\uff1a\u9009\u62e9-phred33\u6216\u8005-phred64\uff0c\u8868\u793a\u6d4b\u5e8f\u5e73\u53f0\u4f7f\u7528\u7684Phred quality score\u3002<\/li>\n<li>--adapter\uff1a\u8f93\u5165adapter\u5e8f\u5217\u3002\u4e5f\u53ef\u4ee5\u4e0d\u8f93\u5165\uff0cTrim Galore!\u4f1a\u81ea\u52a8\u5bfb\u627e\u53ef\u80fd\u6027\u6700\u9ad8\u7684\u5e73\u53f0\u5bf9\u5e94\u7684adapter\u3002\u81ea\u52a8\u641c\u9009\u7684\u5e73\u53f0\u4e09\u4e2a\uff0c\u4e5f\u76f4\u63a5\u8f93\u5165\u8fd9\u4e09\u79cd\u5e73\u53f0\uff0c\u5373--illumina\u3001--nextera\u548c--small_rna\u3002<\/li>\n<li>--stringency\uff1a\u8bbe\u5b9a\u53ef\u4ee5\u5fcd\u53d7\u7684\u524d\u540eadapter\u91cd\u53e0\u7684\u78b1\u57fa\u6570\uff0c\u9ed8\u8ba4\u4e3a1\uff08\u975e\u5e38\u82db\u523b\uff09\u3002\u53ef\u4ee5\u9002\u5ea6\u653e\u5bbd\uff0c\u56e0\u4e3a\u540e\u4e00\u4e2aadapter\u51e0\u4e4e\u4e0d\u53ef\u80fd\u88ab\u6d4b\u5e8f\u4eea\u8bfb\u5230\u3002<\/li>\n<li>--length\uff1a\u8bbe\u5b9a\u8f93\u51fareads\u957f\u5ea6\u9608\u503c\uff0c\u5c0f\u4e8e\u8bbe\u5b9a\u503c\u4f1a\u88ab\u629b\u5f03\u3002<\/li>\n<li>--paired\uff1a\u5bf9\u4e8e\u53cc\u7aef\u6d4b\u5e8f\u7ed3\u679c\uff0c\u4e00\u5bf9reads\u4e2d\uff0c\u5982\u679c\u6709\u4e00\u4e2a\u88ab\u5254\u9664\uff0c\u90a3\u4e48\u53e6\u4e00\u4e2a\u4f1a\u88ab\u540c\u6837\u629b\u5f03\uff0c\u800c\u4e0d\u7ba1\u662f\u5426\u8fbe\u5230\u6807\u51c6\u3002<\/li>\n<li>--retain_unpaired\uff1a\u5bf9\u4e8e\u53cc\u7aef\u6d4b\u5e8f\u7ed3\u679c\uff0c\u4e00\u5bf9reads\u4e2d\uff0c\u5982\u679c\u4e00\u4e2aread\u8fbe\u5230\u6807\u51c6\uff0c\u4f46\u662f\u5bf9\u5e94\u7684\u53e6\u4e00\u4e2a\u8981\u88ab\u629b\u5f03\uff0c\u8fbe\u5230\u6807\u51c6\u7684read\u4f1a\u88ab\u5355\u72ec\u4fdd\u5b58\u4e3a\u4e00\u4e2a\u6587\u4ef6\u3002<\/li>\n<li>--gzip\u548c--dont_gzip\uff1a\u6e05\u6d17\u540e\u7684\u6570\u636ezip\u6253\u5305\u6216\u8005\u4e0d\u6253\u5305\u3002<\/li>\n<li>--output_dir\uff1a\u8f93\u5165\u76ee\u5f55\u3002\u9700\u8981\u63d0\u524d\u5efa\u7acb\u76ee\u5f55\uff0c\u5426\u5219\u8fd0\u884c\u4f1a\u62a5\u9519\u3002<\/li>\n<li>--trim-n : \u79fb\u9664read\u4e00\u7aef\u7684reads<\/li>\n<\/ul>\n<h2>perl\u811a\u672c\u5bf9\u6bcf\u4e2a\u6837\u672c\u751f\u6210shell<\/h2>\n<pre><code>ls ..\/rawdata\/*_R1.fastq.gz|perl -ne &#039;chomp;my $name=$1 if($_=~\/\\\/([^\\\/]+)\\_R1\/);print &quot;trim_galore -q 20 --phred33 --fastqc --illumina --basename $name -j 2 --paired  $name\\_R1.fastq.gz $name\\_R2.fastq.gz \\n&quot;&#039; &gt;trim_galore.sh<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Trim Galore \u53bb\u9664\u63a5\u5934+\u8d28\u63a7\u6d41\u7a0b \u8f6f\u4ef6\u4f7f\u7528\u7b80\u8981\u8bf4\u660e &#8211;quality\uff1a\u8bbe\u5b9aPhred qualit&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-112","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/112","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=112"}],"version-history":[{"count":2,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/112\/revisions"}],"predecessor-version":[{"id":114,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/112\/revisions\/114"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=112"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=112"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=112"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}