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14px;\">\u4f4e\u8d28\u91cf\u7684\u5e8f\u5217\uff1a\u7531\u4e8e\u6d4b\u5e8f\u4eea\u5668\u6216\u53cd\u5e94\u4f53\u7cfb\u7b49\u56e0\u7d20\u7684\u5f71\u54cd\uff0c\u4f1a\u4ea7\u751f\u4e00\u4e9b\u4f4e\u8d28\u91cf\u7684\u6d4b\u5e8f\u5e8f\u5217\uff0c\u8fd9\u4e9b\u5e8f\u5217\u4e0d\u4ec5\u4f1a\u5360\u7528\u670d\u52a1\u5668\u7a7a\u95f4\u548c\u8ba1\u7b97\u8d44\u6e90\uff0c\u4e5f\u4f1a\u5f71\u54cd\u540e\u7eed\u7684\u6570\u636e\u5206\u6790\u7ed3\u679c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8bfb\u957f\u504f\u5dee\uff1a\u7531\u4e8e\u6d4b\u5e8f\u4eea\u5668\u7b49\u56e0\u7d20\u7684\u9650\u5236\uff0c\u6d4b\u5e8f\u6570\u636e\u4e2d\u53ef\u80fd\u5b58\u5728\u957f\u5ea6\u504f\u5dee\uff0c\u5982\u5934\u5c3e\u5e8f\u5217\u8f83\u77ed\u6216\u8f83\u957f\u7b49\uff0c\u8fd9\u4e9b\u504f\u5dee\u4f1a\u5bf9\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u7684\u8ba1\u7b97\u9020\u6210\u5f71\u54cd\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u566a\u58f0\uff1a\u7531\u4e8e\u5b9e\u9a8c\u6761\u4ef6\u7b49\u539f\u56e0\uff0c\u6d4b\u5e8f\u6570\u636e\u4e2d\u5e38\u5e38\u4f1a\u51fa\u73b0\u4e00\u4e9b\u5f02\u8d28\u6027\uff0c\u6bd4\u5982SNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u3001INDEL\uff08\u63d2\u5165\/\u7f3a\u5931\uff09\u7b49\uff0c\u8fd9\u4e9b\u5f02\u8d28\u6027\u4f1a\u5f71\u54cd\u540e\u7eed\u7684\u5dee\u5f02\u5206\u6790\u548c\u529f\u80fd\u6ce8\u91ca\u3002<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u56e0\u6b64\uff0c\u6211\u4eec\u9700\u8981\u5bf9\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\uff0c\u53bb\u9664\u6389\u4f4e\u8d28\u91cf\u7684\u5e8f\u5217\u548c\u566a\u58f0\uff0c\u63d0\u9ad8\u6570\u636e\u7684\u53ef\u9760\u6027\u548c\u51c6\u786e\u6027\u3002<\/span><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u4e09\u3001\u5982\u4f55\u5bf9\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\uff1f<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u76ee\u524d\uff0c\u6709\u5f88\u591a\u5de5\u5177\u53ef\u4ee5\u5bf9\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\u3002\u5176\u4e2d\u6bd4\u8f83\u5e38\u7528\u7684\u5de5\u5177\u5305\u62ecTrimmomatic\u3001Fastp\u548cCutadapt\u7b49\u3002\u4e0b\u9762\u5c0f\u679c\u4ee5Trimmomatic\u4e3a\u4f8b\uff0c\u4ecb\u7ecd\u5982\u4f55\u5bf9\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">1.\u51c6\u5907\u5de5\u4f5c\uff1a\u4ecd\u7136\u662f\u7528miniconda\u5b89\u88c5Trimmomatic<\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">conda create \u2013name trimmomatic<\/span><\/code><code><span class=\"code-snippet_outer\">conda activate trimmomatic<\/span><\/code><code><span class=\"code-snippet_outer\">conda install -c bioconda trimmomatic<\/span><\/code><code><span class=\"code-snippet_outer\">trimmomatic -version<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u53ef\u4ee5\u770b\u5230\u5b89\u88c5\u6210\u529f\uff0c\u7248\u672c\u4e3a0.39<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">2. \u8fd0\u884cTrimmomatic<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5bf9\u4e8e\u53cc\u672b\u7aef\u6d4b\u5e8f\u6765\u8bf4\uff0c\u53ef\u4ee5\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">java -jar trimmomatic<span class=\"code-snippet__number\">-0.39<\/span>.jar PE input_forward.fq.gz input_reverse.fq.gz<\/span><\/code><code><span class=\"code-snippet_outer\">output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:<span class=\"code-snippet__number\">2<\/span>:<span class=\"code-snippet__number\">30<\/span>:<span class=\"code-snippet__number\">10<\/span>:<span class=\"code-snippet__number\">2<\/span>:True LEADING:<span class=\"code-snippet__number\">3<\/span> TRAILING:<span class=\"code-snippet__number\">3<\/span> MINLEN:<span class=\"code-snippet__number\">36<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4e3a\u4e86\u65b9\u4fbf\u7406\u89e3\u5c0f\u679c\u5c06\u89e3\u91ca\u653e\u5728\u4e0b\u9762\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">input_forward.fq.gz \u548c input_reverse.fq.gz\u662f\u6307\u8f93\u5165\u7684\u53cc\u7aef\u6d4b\u5e8f\u6570\u636e\uff0c\u5305\u62ec forward \u548creverse reads\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">output_forward_paired.fq.gz \u548c output_reverse_paired.fq.gz\u662f\u6307\u8f93\u51fa\u7684\u8fc7\u6ee4\u540e\u7684\u53cc\u7aef\u6d4b\u5e8f\u6570\u636e\uff0c\u5305\u62ec forward \u548c reverse reads\uff0c\u4e14\u4e24\u7aef reads \u5747\u901a\u8fc7\u8d28\u91cf\u63a7\u5236\u548c\u8fc7\u6ee4\u3002output_forward_unpaired.fq.gz \u548c output_reverse_unpaired.fq.gz\u6307\u8f93\u51fa\u7684\u672a\u5339\u914d\u7684reads\uff0c\u5176\u4e2doutput_forward_unpaired.fq.gz \u5305\u62ec\u672a\u5339\u914d\u7684 forward reads\uff0c output_reverse_unpaired.fq.gz \u5305\u62ec\u672a\u5339\u914d\u7684 reverse reads\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">ILLUMINACLIP:TruSeq3-PE.fa:<span class=\"code-snippet__number\">2<\/span>:<span class=\"code-snippet__number\">30<\/span>:<span class=\"code-snippet__number\">10<\/span>:<span class=\"code-snippet__number\">2<\/span>:True: \u4f7f\u7528 TruSeq3-PE.fa \u4f5c\u4e3a adapter \u5e8f\u5217\u6587\u4ef6\uff0c\u8bbe\u5b9a\u7684\u53c2\u6570\u4f9d\u6b21\u4e3a\uff1a<span class=\"code-snippet__function\">seed <span class=\"code-snippet__title\">mismatches<\/span> <span class=\"code-snippet__params\">(<span class=\"code-snippet__number\">2<\/span>)<\/span>, palindrome clip <span class=\"code-snippet__title\">threshold<\/span> <span class=\"code-snippet__params\">(<span class=\"code-snippet__number\">30<\/span>)<\/span>, simple clip <span class=\"code-snippet__title\">threshold<\/span> <span class=\"code-snippet__params\">(<span class=\"code-snippet__number\">10<\/span>)<\/span>, keep both <span class=\"code-snippet__title\">reads<\/span> <span class=\"code-snippet__params\">(True)<\/span>\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">LEADING:3: \u5c06 reads \u5f00\u5934\u7684\u8d28\u91cf\u503c\u4f4e\u4e8e 3 \u7684\u90e8\u5206\u5207\u9664\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">TRAILING:3: \u5c06 reads \u672b\u5c3e\u7684\u8d28\u91cf\u503c\u4f4e\u4e8e 3 \u7684\u90e8\u5206\u5207\u9664\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">MINLEN:36: \u4e22\u5f03\u957f\u5ea6\u5c0f\u4e8e 36 bp \u7684 reads\u3002<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">!!!\u6ce8\u610f\uff1a\u5c0f\u679c\u9ad8\u4eae\u7684\u4e24\u4e2a\u6587\u4ef6\uff0c\u5728\u6267\u884c\u547d\u4ee4\u65f6\u8981\u8f93\u5165\u6b63\u786e\u7684\u6587\u4ef6\u8def\u5f84\u548c\u6587\u4ef6\u540d\u79f0\u3002\u53e6\u5916\u56e0\u4e3a\u5728\u5b9e\u9645\u5de5\u4f5c\u4e2d\u6211\u4eec\u5f80\u5f80\u9700\u8981\u5904\u7406\u5f88\u591a\u6570\u636e\uff0c\u6bd4\u5982\u8fd9\u6b21\u5c0f\u679c\u51c6\u5907\u8fc7\u6ee49\u4e2a\u6587\u4ef6\uff0c\u6bcf\u4e2a.sra\u6587\u4ef6\u53c8\u8f6c\u5316\u4e3a\u4e86read1\uff0cread2\u4e24\u4e2a\u6587\u4ef6\uff0c\u6240\u4ee5\u5c0f\u679c\u4e3a\u4e86\u5077\u61d2\u5199\u4e86\u4e2a\u811a\u672c\uff0c\u4e00\u6b21\u6027\u8fc7\u6ee4\u6240\u6709\u6570\u636e\uff0c\u811a\u672c\u652f\u6301\u53cc\u7aef\u6d4b\u5e8f\uff0c\u8fc7\u6ee4\u7684\u6570\u636e\u653e\u5728\u540c\u4e00\u4e2a\u6587\u4ef6\u5939\u4e0b\uff0c\u5176\u4e2d\u7684\u8def\u5f84\u6839\u636e\u81ea\u5df1\u7684\u4fee\u6539\u5373\u53ef\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u811a\u672c\u5982\u4e0b\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#!\/bin\/bash<\/span><\/code><code><span class=\"code-snippet_outer\"># \u5b9a\u4e49\u8f93\u5165\u548c\u8f93\u51fa\u76ee\u5f55<\/span><\/code><code><span class=\"code-snippet_outer\">input_dir=~\/my_folder\/trimm<\/span><\/code><code><span class=\"code-snippet_outer\">output_dir=~\/my_folder\/trimm\/ninanjie_output<\/span><\/code><code><span class=\"code-snippet_outer\"># \u904d\u5386\u8f93\u5165\u76ee\u5f55\u4e2d\u4ee5 _1.fastq \u7ed3\u5c3e\u7684\u6240\u6709\u6587\u4ef6.gz<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> file1 in ${input_dir}<span class=\"code-snippet__comment\">\/*_1.fastq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">do<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> # \u83b7\u53d6\u57fa\u672c\u6587\u4ef6\u540d\uff08\u5220\u9664 _1.fastq.gz \u6269\u5c55\u540d\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> base=$(basename ${file1} _1.fastq.gz)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> # \u5b9a\u4e49\u76f8\u5e94\u6587\u4ef62\u7684\u8def\u5f84<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> file2=${input_dir}\/${base}_2.fastq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> # \u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> out_forward_paired=${output_dir}\/${base}_forward_paired.fq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> out_forward_unpaired=${output_dir}\/${base}_forward_unpaired.fq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> out_reverse_paired=${output_dir}\/${base}_reverse_paired.fq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> out_reverse_unpaired=${output_dir}\/${base}_reverse_unpaired.fq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> # \u4f7f\u7528nohup\u5728\u540e\u53f0\u8fd0\u884cTrimmomatic<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> nohup java -jar \/media\/desk16\/iyun003\/miniconda3\/envs\/trimmomatic\/share\/trimmomatic-0.39-2\/trimmomatic.jar <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> PE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${file1} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${file2} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${out_forward_paired} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${out_forward_unpaired} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${out_reverse_paired} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${out_reverse_unpaired} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">ILLUMINACLIP:\/media\/desk16\/iyun003\/miniconda3\/envs\/trimmomatic\/share\/trimmomatic-0.39-2\/adapters\/TruSeq3-PE.fa:2:30:10:2:True <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> LEADING:3 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> TRAILING:3 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> MINLEN:36 > ${output_dir}\/${base}_trimmomatic.log 2>&1 &<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">Done<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u67e5\u770b\u5176\u4e2d\u4e00\u4e2a\u6587\u4ef6\u7684\u65e5\u5fd7\uff0c\u6700\u540e\u4e00\u884c\u663e\u793a\u6210\u529f\uff01\u5c0f\u679c\u6cea\u76ee\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u90e8\u5206\u8f93\u51fa\u7ed3\u679c<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5355\u672b\u7aef\u6d4b\u5e8f\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">java -jar trimmomatic<span class=\"code-snippet__number\">-0.35<\/span>.jar SE -phred33 input.fq.gz output.fq.gz<\/span><\/code><code><span class=\"code-snippet_outer\">ILLUMINACLIP:TruSeq3-SE:<span class=\"code-snippet__number\">2<\/span>:<span class=\"code-snippet__number\">30<\/span>:<span class=\"code-snippet__number\">10<\/span> LEADING:<span class=\"code-snippet__number\">3<\/span> TRAILING:<span class=\"code-snippet__number\">3<\/span> SLIDINGWINDOW:<span class=\"code-snippet__number\">4<\/span>:<span class=\"code-snippet__number\">15<\/span> MINLEN:<span class=\"code-snippet__number\">36<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd8\u662f\u4e00\u6837\u6ce8\u610f\u4fee\u6539\u6587\u4ef6\u8def\u5f84\u548c\u6587\u4ef6\u540d\u79f0\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u597d\u5566\uff0c\u4e0d\u591a\u8bf4\u4e86\uff0c\u4eca\u5929\u7684\u5185\u5bb9\u5c31\u5230\u8fd9\u91cc\u4e86\uff0c\u4f60\u5b66\u4f1a\u4e86\u5417\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5982\u679c\u60f3\u7528\u670d\u52a1\u5668\u53ef\u4ee5\u8054\u7cfb\u5fae\u4fe1\uff1a18502195490\uff08\u5feb\u6765\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u5427\uff01\uff09<\/span><span style=\"text-align: center;letter-spacing: 0.578px;\"><\/span><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section data-tools=\"135\u7f16\u8f91\u5668\" data-id=\"105054\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section style=\"margin: 10px auto;text-align: center;\">\n<section style=\"padding-top: 30px;padding-bottom: 30px;background-color: rgb(242, 246, 255);border-radius: 7px;\">\n<section style=\"display: flex;justify-content: space-evenly;align-items: center;\">\n<section data-width=\"26%\" style=\"width: 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[…]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59104"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=59104"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59104\/revisions"}],"predecessor-version":[{"id":59107,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59104\/revisions\/59107"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59104"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59104"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59104"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":59104,"date":"2024-06-17T07:37:44","date_gmt":"2024-06-16T23:37:44","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59104"},"modified":"2024-06-17T07:37:44","modified_gmt":"2024-06-16T23:37:44","slug":"%e5%88%a9%e7%94%a8trimmomatic%e8%bf%9b%e8%a1%8c%e8%bd%ac%e5%bd%95%e7%bb%84%e5%8e%9f%e5%a7%8b%e6%95%b0%e6%8d%ae%e8%bf%87%e6%bb%a4%ef%bc%9a%e5%b0%8f%e6%9e%9c%e5%90%90%e8%a1%80%e6%95%b4%e7%90%86%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59104","title":{"rendered":"\u5229\u7528Trimmomatic\u8fdb\u884c\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fc7\u6ee4\uff1a\u5c0f\u679c\u5410\u8840\u6574\u7406\uff01"},"content":{"rendered":"

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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"\u5229\u7528Trimmomatic\u8fdb\u884c\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fc7\u6ee4\uff1a\u5c0f\u679c\u5410\u8840\u6574\u7406\uff01\",\"time\":\"2023-06-24 19:00:08\",\"timeStamp\":\"1687604408\"};\n<\/script><br \/>\n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488614&idx=1&sn=9c9f393215f61b122064e9587db20a5d&chksm=cf7c84a3f80b0db5122645aeb126e84f25a5e6ce7b46171865add254879afe38025c38248d0d#rd\" target=\"_blank\" rel=\"noopener\">\u5229\u7528Trimmomatic\u8fdb\u884c\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fc7\u6ee4\uff1a\u5c0f\u679c\u5410\u8840\u6574\u7406\uff01<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span id=\"copyright_logo\" class=\"wx_tap_link js_wx_tap_highlight rich_media_meta icon_appmsg_tag appmsg_title_tag weui-wa-hotarea\">\u539f\u521b <\/span><span class=\"rich_media_meta 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data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-role=\"list\">\n<section style=\"font-size: 16px;\">\n<section style=\"margin: 10px 0% 8px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;padding-left: 8px;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"letter-spacing: 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14px;\">\u56e0\u6b64\uff0c\u5728\u8fdb\u884c\u8fdb\u4e00\u6b65\u7684\u5dee\u5f02\u5206\u6790\u3001\u529f\u80fd\u6ce8\u91ca\u548c\u751f\u4fe1\u5206\u6790\u4e4b\u524d\uff0c\u6211\u4eec\u9700\u8981\u5bf9\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\uff0c\u53bb\u9664\u6389\u4f4e\u8d28\u91cf\u7684\u5e8f\u5217\u548c\u566a\u58f0\uff0c\u63d0\u9ad8\u6570\u636e\u7684\u53ef\u9760\u6027\u548c\u51c6\u786e\u6027\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u4e00\u3001\u4ec0\u4e48\u662f\u8f6c\u5f55\u7ec4<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8f6c\u5f55\u7ec4\u662f\u6307\u5728\u4e00\u4e2a\u65f6\u523b\u5185\u7ec6\u80de\u5185\u8f6c\u5f55\u751f\u6210\u7684RNA\u7684\u603b\u548c\u3002\u4e0e\u57fa\u56e0\u7ec4\u76f8\u6bd4\uff0c\u8f6c\u5f55\u7ec4\u66f4\u53cd\u6620\u4e86\u7ec6\u80de\u5185\u57fa\u56e0\u7684\u8868\u8fbe\u60c5\u51b5\uff0c\u80fd\u591f\u4e3a\u6211\u4eec\u63ed\u793a\u7ec6\u80de\u5185\u90e8\u7684\u57fa\u56e0\u8c03\u63a7\u7f51\u7edc\u4ee5\u53ca\u57fa\u56e0\u529f\u80fd\u7684\u53d8\u5316\u3002\u56e0\u6b64\uff0c\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u5df2\u7ecf\u6210\u4e3a\u7814\u7a76\u57fa\u56e0\u529f\u80fd\u548c\u57fa\u56e0\u8c03\u63a7\u673a\u5236\u7684\u91cd\u8981\u624b\u6bb5\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u4e8c\u3001\u4e3a\u4ec0\u4e48\u8981\u8fc7\u6ee4\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\uff1f<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u4ea7\u751f\u7684\u539f\u59cb\u6570\u636e\u5f80\u5f80\u5177\u6709\u4ee5\u4e0b\u95ee\u9898\uff1a<\/span><\/p>\n<\/section>\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;border-width: 1px;border-style: solid;border-color: black;padding: 10px;box-shadow: rgb(204, 204, 204) 0.2em 0.2em 0.3em;\">\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4f4e\u8d28\u91cf\u7684\u5e8f\u5217\uff1a\u7531\u4e8e\u6d4b\u5e8f\u4eea\u5668\u6216\u53cd\u5e94\u4f53\u7cfb\u7b49\u56e0\u7d20\u7684\u5f71\u54cd\uff0c\u4f1a\u4ea7\u751f\u4e00\u4e9b\u4f4e\u8d28\u91cf\u7684\u6d4b\u5e8f\u5e8f\u5217\uff0c\u8fd9\u4e9b\u5e8f\u5217\u4e0d\u4ec5\u4f1a\u5360\u7528\u670d\u52a1\u5668\u7a7a\u95f4\u548c\u8ba1\u7b97\u8d44\u6e90\uff0c\u4e5f\u4f1a\u5f71\u54cd\u540e\u7eed\u7684\u6570\u636e\u5206\u6790\u7ed3\u679c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8bfb\u957f\u504f\u5dee\uff1a\u7531\u4e8e\u6d4b\u5e8f\u4eea\u5668\u7b49\u56e0\u7d20\u7684\u9650\u5236\uff0c\u6d4b\u5e8f\u6570\u636e\u4e2d\u53ef\u80fd\u5b58\u5728\u957f\u5ea6\u504f\u5dee\uff0c\u5982\u5934\u5c3e\u5e8f\u5217\u8f83\u77ed\u6216\u8f83\u957f\u7b49\uff0c\u8fd9\u4e9b\u504f\u5dee\u4f1a\u5bf9\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u7684\u8ba1\u7b97\u9020\u6210\u5f71\u54cd\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u566a\u58f0\uff1a\u7531\u4e8e\u5b9e\u9a8c\u6761\u4ef6\u7b49\u539f\u56e0\uff0c\u6d4b\u5e8f\u6570\u636e\u4e2d\u5e38\u5e38\u4f1a\u51fa\u73b0\u4e00\u4e9b\u5f02\u8d28\u6027\uff0c\u6bd4\u5982SNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u3001INDEL\uff08\u63d2\u5165\/\u7f3a\u5931\uff09\u7b49\uff0c\u8fd9\u4e9b\u5f02\u8d28\u6027\u4f1a\u5f71\u54cd\u540e\u7eed\u7684\u5dee\u5f02\u5206\u6790\u548c\u529f\u80fd\u6ce8\u91ca\u3002<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u56e0\u6b64\uff0c\u6211\u4eec\u9700\u8981\u5bf9\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\uff0c\u53bb\u9664\u6389\u4f4e\u8d28\u91cf\u7684\u5e8f\u5217\u548c\u566a\u58f0\uff0c\u63d0\u9ad8\u6570\u636e\u7684\u53ef\u9760\u6027\u548c\u51c6\u786e\u6027\u3002<\/span><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u4e09\u3001\u5982\u4f55\u5bf9\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\uff1f<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u76ee\u524d\uff0c\u6709\u5f88\u591a\u5de5\u5177\u53ef\u4ee5\u5bf9\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\u3002\u5176\u4e2d\u6bd4\u8f83\u5e38\u7528\u7684\u5de5\u5177\u5305\u62ecTrimmomatic\u3001Fastp\u548cCutadapt\u7b49\u3002\u4e0b\u9762\u5c0f\u679c\u4ee5Trimmomatic\u4e3a\u4f8b\uff0c\u4ecb\u7ecd\u5982\u4f55\u5bf9\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8fc7\u6ee4\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">1.\u51c6\u5907\u5de5\u4f5c\uff1a\u4ecd\u7136\u662f\u7528miniconda\u5b89\u88c5Trimmomatic<\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">conda create \u2013name trimmomatic<\/span><\/code><code><span class=\"code-snippet_outer\">conda activate trimmomatic<\/span><\/code><code><span class=\"code-snippet_outer\">conda install -c bioconda trimmomatic<\/span><\/code><code><span class=\"code-snippet_outer\">trimmomatic -version<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u53ef\u4ee5\u770b\u5230\u5b89\u88c5\u6210\u529f\uff0c\u7248\u672c\u4e3a0.39<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">2. \u8fd0\u884cTrimmomatic<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5bf9\u4e8e\u53cc\u672b\u7aef\u6d4b\u5e8f\u6765\u8bf4\uff0c\u53ef\u4ee5\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">java -jar trimmomatic<span class=\"code-snippet__number\">-0.39<\/span>.jar PE input_forward.fq.gz input_reverse.fq.gz<\/span><\/code><code><span class=\"code-snippet_outer\">output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:<span class=\"code-snippet__number\">2<\/span>:<span class=\"code-snippet__number\">30<\/span>:<span class=\"code-snippet__number\">10<\/span>:<span class=\"code-snippet__number\">2<\/span>:True LEADING:<span class=\"code-snippet__number\">3<\/span> TRAILING:<span class=\"code-snippet__number\">3<\/span> MINLEN:<span class=\"code-snippet__number\">36<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4e3a\u4e86\u65b9\u4fbf\u7406\u89e3\u5c0f\u679c\u5c06\u89e3\u91ca\u653e\u5728\u4e0b\u9762\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">input_forward.fq.gz \u548c input_reverse.fq.gz\u662f\u6307\u8f93\u5165\u7684\u53cc\u7aef\u6d4b\u5e8f\u6570\u636e\uff0c\u5305\u62ec forward \u548creverse reads\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">output_forward_paired.fq.gz \u548c output_reverse_paired.fq.gz\u662f\u6307\u8f93\u51fa\u7684\u8fc7\u6ee4\u540e\u7684\u53cc\u7aef\u6d4b\u5e8f\u6570\u636e\uff0c\u5305\u62ec forward \u548c reverse reads\uff0c\u4e14\u4e24\u7aef reads \u5747\u901a\u8fc7\u8d28\u91cf\u63a7\u5236\u548c\u8fc7\u6ee4\u3002output_forward_unpaired.fq.gz \u548c output_reverse_unpaired.fq.gz\u6307\u8f93\u51fa\u7684\u672a\u5339\u914d\u7684reads\uff0c\u5176\u4e2doutput_forward_unpaired.fq.gz \u5305\u62ec\u672a\u5339\u914d\u7684 forward reads\uff0c output_reverse_unpaired.fq.gz \u5305\u62ec\u672a\u5339\u914d\u7684 reverse reads\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">ILLUMINACLIP:TruSeq3-PE.fa:<span class=\"code-snippet__number\">2<\/span>:<span class=\"code-snippet__number\">30<\/span>:<span class=\"code-snippet__number\">10<\/span>:<span class=\"code-snippet__number\">2<\/span>:True: \u4f7f\u7528 TruSeq3-PE.fa \u4f5c\u4e3a adapter \u5e8f\u5217\u6587\u4ef6\uff0c\u8bbe\u5b9a\u7684\u53c2\u6570\u4f9d\u6b21\u4e3a\uff1a<span class=\"code-snippet__function\">seed <span class=\"code-snippet__title\">mismatches<\/span> <span class=\"code-snippet__params\">(<span class=\"code-snippet__number\">2<\/span>)<\/span>, palindrome clip <span class=\"code-snippet__title\">threshold<\/span> <span class=\"code-snippet__params\">(<span class=\"code-snippet__number\">30<\/span>)<\/span>, simple clip <span class=\"code-snippet__title\">threshold<\/span> <span class=\"code-snippet__params\">(<span class=\"code-snippet__number\">10<\/span>)<\/span>, keep both <span class=\"code-snippet__title\">reads<\/span> <span class=\"code-snippet__params\">(True)<\/span>\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">LEADING:3: \u5c06 reads \u5f00\u5934\u7684\u8d28\u91cf\u503c\u4f4e\u4e8e 3 \u7684\u90e8\u5206\u5207\u9664\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">TRAILING:3: \u5c06 reads \u672b\u5c3e\u7684\u8d28\u91cf\u503c\u4f4e\u4e8e 3 \u7684\u90e8\u5206\u5207\u9664\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">MINLEN:36: \u4e22\u5f03\u957f\u5ea6\u5c0f\u4e8e 36 bp \u7684 reads\u3002<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">!!!\u6ce8\u610f\uff1a\u5c0f\u679c\u9ad8\u4eae\u7684\u4e24\u4e2a\u6587\u4ef6\uff0c\u5728\u6267\u884c\u547d\u4ee4\u65f6\u8981\u8f93\u5165\u6b63\u786e\u7684\u6587\u4ef6\u8def\u5f84\u548c\u6587\u4ef6\u540d\u79f0\u3002\u53e6\u5916\u56e0\u4e3a\u5728\u5b9e\u9645\u5de5\u4f5c\u4e2d\u6211\u4eec\u5f80\u5f80\u9700\u8981\u5904\u7406\u5f88\u591a\u6570\u636e\uff0c\u6bd4\u5982\u8fd9\u6b21\u5c0f\u679c\u51c6\u5907\u8fc7\u6ee49\u4e2a\u6587\u4ef6\uff0c\u6bcf\u4e2a.sra\u6587\u4ef6\u53c8\u8f6c\u5316\u4e3a\u4e86read1\uff0cread2\u4e24\u4e2a\u6587\u4ef6\uff0c\u6240\u4ee5\u5c0f\u679c\u4e3a\u4e86\u5077\u61d2\u5199\u4e86\u4e2a\u811a\u672c\uff0c\u4e00\u6b21\u6027\u8fc7\u6ee4\u6240\u6709\u6570\u636e\uff0c\u811a\u672c\u652f\u6301\u53cc\u7aef\u6d4b\u5e8f\uff0c\u8fc7\u6ee4\u7684\u6570\u636e\u653e\u5728\u540c\u4e00\u4e2a\u6587\u4ef6\u5939\u4e0b\uff0c\u5176\u4e2d\u7684\u8def\u5f84\u6839\u636e\u81ea\u5df1\u7684\u4fee\u6539\u5373\u53ef\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u811a\u672c\u5982\u4e0b\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#!\/bin\/bash<\/span><\/code><code><span class=\"code-snippet_outer\"># \u5b9a\u4e49\u8f93\u5165\u548c\u8f93\u51fa\u76ee\u5f55<\/span><\/code><code><span class=\"code-snippet_outer\">input_dir=~\/my_folder\/trimm<\/span><\/code><code><span class=\"code-snippet_outer\">output_dir=~\/my_folder\/trimm\/ninanjie_output<\/span><\/code><code><span class=\"code-snippet_outer\"># \u904d\u5386\u8f93\u5165\u76ee\u5f55\u4e2d\u4ee5 _1.fastq \u7ed3\u5c3e\u7684\u6240\u6709\u6587\u4ef6.gz<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> file1 in ${input_dir}<span class=\"code-snippet__comment\">\/*_1.fastq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">do<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> # \u83b7\u53d6\u57fa\u672c\u6587\u4ef6\u540d\uff08\u5220\u9664 _1.fastq.gz \u6269\u5c55\u540d\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> base=$(basename ${file1} _1.fastq.gz)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> # \u5b9a\u4e49\u76f8\u5e94\u6587\u4ef62\u7684\u8def\u5f84<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> file2=${input_dir}\/${base}_2.fastq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> # \u5b9a\u4e49\u8f93\u51fa\u6587\u4ef6\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> out_forward_paired=${output_dir}\/${base}_forward_paired.fq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> out_forward_unpaired=${output_dir}\/${base}_forward_unpaired.fq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> out_reverse_paired=${output_dir}\/${base}_reverse_paired.fq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> out_reverse_unpaired=${output_dir}\/${base}_reverse_unpaired.fq.gz<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> # \u4f7f\u7528nohup\u5728\u540e\u53f0\u8fd0\u884cTrimmomatic<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> nohup java -jar \/media\/desk16\/iyun003\/miniconda3\/envs\/trimmomatic\/share\/trimmomatic-0.39-2\/trimmomatic.jar <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> PE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${file1} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${file2} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${out_forward_paired} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${out_forward_unpaired} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${out_reverse_paired} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> ${out_reverse_unpaired} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">ILLUMINACLIP:\/media\/desk16\/iyun003\/miniconda3\/envs\/trimmomatic\/share\/trimmomatic-0.39-2\/adapters\/TruSeq3-PE.fa:2:30:10:2:True <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> LEADING:3 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> TRAILING:3 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"> MINLEN:36 > ${output_dir}\/${base}_trimmomatic.log 2>&1 &<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">Done<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u67e5\u770b\u5176\u4e2d\u4e00\u4e2a\u6587\u4ef6\u7684\u65e5\u5fd7\uff0c\u6700\u540e\u4e00\u884c\u663e\u793a\u6210\u529f\uff01\u5c0f\u679c\u6cea\u76ee\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u90e8\u5206\u8f93\u51fa\u7ed3\u679c<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5355\u672b\u7aef\u6d4b\u5e8f\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">java -jar trimmomatic<span class=\"code-snippet__number\">-0.35<\/span>.jar SE -phred33 input.fq.gz output.fq.gz<\/span><\/code><code><span class=\"code-snippet_outer\">ILLUMINACLIP:TruSeq3-SE:<span class=\"code-snippet__number\">2<\/span>:<span class=\"code-snippet__number\">30<\/span>:<span class=\"code-snippet__number\">10<\/span> LEADING:<span class=\"code-snippet__number\">3<\/span> TRAILING:<span class=\"code-snippet__number\">3<\/span> SLIDINGWINDOW:<span class=\"code-snippet__number\">4<\/span>:<span class=\"code-snippet__number\">15<\/span> MINLEN:<span class=\"code-snippet__number\">36<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd8\u662f\u4e00\u6837\u6ce8\u610f\u4fee\u6539\u6587\u4ef6\u8def\u5f84\u548c\u6587\u4ef6\u540d\u79f0\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u597d\u5566\uff0c\u4e0d\u591a\u8bf4\u4e86\uff0c\u4eca\u5929\u7684\u5185\u5bb9\u5c31\u5230\u8fd9\u91cc\u4e86\uff0c\u4f60\u5b66\u4f1a\u4e86\u5417\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5982\u679c\u60f3\u7528\u670d\u52a1\u5668\u53ef\u4ee5\u8054\u7cfb\u5fae\u4fe1\uff1a18502195490\uff08\u5feb\u6765\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u5427\uff01\uff09<\/span><span style=\"text-align: center;letter-spacing: 0.578px;\"><\/span><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section data-tools=\"135\u7f16\u8f91\u5668\" data-id=\"105054\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section style=\"margin: 10px auto;text-align: center;\">\n<section style=\"padding-top: 30px;padding-bottom: 30px;background-color: rgb(242, 246, 255);border-radius: 7px;\">\n<section style=\"display: flex;justify-content: space-evenly;align-items: center;\">\n<section data-width=\"26%\" style=\"width: 150.266px;\">\n<section style=\"padding: 7px;border-radius: 15px;box-shadow: rgba(169, 187, 223, 0.45) 4px 4px 8px, rgb(255, 255, 255) -2.5px -2.5px 5px;\">\n<section data-width=\"100%\" style=\"width: 136.266px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"136\" data-cropsely1=\"0\" data-cropsely2=\"137\" data-ratio=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_jEYQoRbKh3HUg3IGgzymibpTnmaM6Q-2.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwIX3hF1ZZeqvXLknM5Oq7CDG9YFpmvU1ge12vc3NvibhViceQjEYQoRbKh3HUg3IGgzymibpTnmaM6Q\/640?wx_fmt=jpeg'\" data-type=\"png\" data-w=\"430\" data-width=\"100%\" style=\"height: 137px;vertical-align: inherit;width: 137px;display: block;border-radius: 7px;\" title=\"\u5c0f\u4e91-\u5fae\u4fe1\u4e8c\u7ef4\u7801.png\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section data-width=\"62%\" style=\"width: 358.359px;\">\n<section style=\"display: inline-block;\">\n<section style=\"padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><span style=\"letter-spacing: 1.5px;\">\u626b\u7801\u52a0\u5c0f\u679c<\/span><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><span style=\"letter-spacing: 1.5px;\">\u9886\u53d6\u751f\u4fe1\u5927\u793c\u5305<\/span><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><span style=\"letter-spacing: 0.5px;text-indent: 0em;\"><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5229\u7528Trimmomatic\u8fdb\u884c\u8f6c\u5f55\u7ec4\u539f\u59cb\u6570\u636e\u8fc7\u6ee4\uff1a\u5c0f\u679c\u5410\u8840\u6574\u7406\uff01 \u539f\u521b \u5c0f\u679c […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59104"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=59104"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59104\/revisions"}],"predecessor-version":[{"id":59107,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59104\/revisions\/59107"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59104"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59104"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59104"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}