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left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;width: 403.391px;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;\">\n<section style=\"margin-top: 10px;\">\n<section style=\"text-align: center;\">\n<section style=\"font-size: 16px;\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;vertical-align: top;width: 70.0348%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70.0348% !important;\">\n<section style=\"margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\"> 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10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;line-height: 0;\">\n<section>\n<section style=\"display: inline-block;vertical-align: middle;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 0;\">\n<section style=\"width: 111px;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1.75em;text-indent: 0em;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;height: auto;width: 111px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_GBhsibRAgNiaQsH4ichdP9ibEhHMFA-108.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyL6u7wJswOp8vtpzGp6vYngnlT6jiavu08Bvp2iblzGf3IkoBD9NGBhsibRAgNiaQsH4ichdP9ibEhHMFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"400\" style=\"vertical-align: middle;width: 100%;\" 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>\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 8px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"padding-left: 8px;display: inline-block;width: 578px;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;\">\n<p><span style=\"letter-spacing: 0.578px;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;\"><span style=\"font-size: 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14px;\">\u5b83\u53ef\u4ee5\u5bf9Illumina\u5e73\u53f0\u7684\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u3001\u8fc7\u6ee4\u4f4e\u8d28\u91cf\u5e8f\u5217\u3001\u622a\u65ad3’\u7aef\u4f4e\u8d28\u91cf\u5e8f\u5217\u3001\u53bb\u9664\u63a5\u5934\u5e8f\u5217\u7b49\u64cd\u4f5c\uff0c\u540c\u65f6\u8fd8\u53ef\u4ee5\u7edf\u8ba1\u5e8f\u5217\u8d28\u91cf\u5206\u5e03\u3001GC\u542b\u91cf\u5206\u5e03\u3001\u9519\u8bef\u7387\u5206\u5e03\u3001N\u542b\u91cf\u7b49\u4fe1\u606f\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;\">fastp\u91c7\u7528\u591a\u7ebf\u7a0b\u52a0\u901f\uff0c\u901f\u5ea6\u5feb\u3001\u51c6\u786e\u6027\u9ad8\uff0c\u5e76\u4e14\u652f\u6301\u591a\u79cd\u6570\u636e\u8f93\u5165\u548c\u8f93\u51fa\u683c\u5f0f\u3002\u4eca\u5929\u5c0f\u679c\u60f3\u5e26\u5927\u5bb6\u4e00\u8d77\u5b66\u4e60\u4e0b\u5982\u4f55\u7528fastp\u5bf9\u539f\u59cb\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u4e0b\u9762\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_fGErXbNqg62srzJVuGIw5CCF0DaBQg-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAzUmbl9AKuU2I0OTXNMqJibibG7LAuZZgjC83Ks5xTRdGYPsQfGErXbNqg62srzJVuGIw5CCF0DaBQg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u6570\u636e\u51c6\u5907<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5728ncbi\u7684sra\u6570\u636e\u5e93\u4e0b\u8f7d\u7684\u62df\u5357\u82a5\u6d4b\u5e8f\u6570\u636e\uff0c\u5305\u62ec\u56db\u4e2a\u57fa\u56e0\u578b\uff0c\u6bcf\u4e2a\u57fa\u56e0\u578b\u4e94\u4e2a\u91cd\u590d\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u94fe\u63a5\u5728\u8fd9\u91cc\uff0c\u5c0f\u679c\u4f7f\u7528\u7684\u6837\u672c\u7f16\u53f7\u4e3a<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">\uff08ERR9708198,ERR9708199,ERR9708200,ERR9708201,ERR9708202,ERR9708297,ERR9708298,ERR9708299,ERR9708300,ERR9708301,ERR9708388,ERR9708389,ERR9708390,ERR9708391,ERR9708392,ERR9708690,ERR9708691,ERR9708692,ERR9708693,ERR9708694\uff09<\/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;\">\u6570\u636e\u7684\u5177\u4f53\u4e0b\u8f7d\u65b9\u6cd5\u53ef\u4ee5\u67e5\u770b\u5f80\u671f\u5185\u5bb9\uff1a\u5c0f\u679c\u53d1\u73b0\u7528SRA Toolkit\u5de5\u5177\u4e0b\u8f7d\u8f6c\u5f55\u7ec4\u6570\u636e\u5f88\u597d\u7528\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd9\u91cc\u5c31\u4e0d\u518d\u8d58\u8ff0\u4e86\uff0c\u76f4\u63a5\u653e\u4ee3\u7801\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">nohup prefetch -O . $(<srr_acc_list.txt) &<=<span class=\"code-snippet__string\">\"\"<\/span> span=<span class=\"code-snippet__string\">\"\"<\/span>><\/span><\/code><code><span class=\"code-snippet_outer\">fastq-dump --gzip --split-files *.sra &<\/span><\/code><code><span class=\"code-snippet_outer\">gunzip *.fastq.gz<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\" powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"line-height: 0;text-align: center;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_gA7tHx97zkib2hlfDS6YtSJ2DPHxcQ-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAzUmbl9AKuU2I0OTXNMqJibibHmPicgof4fsMCDqBAdp8ByubHRgA7tHx97zkib2hlfDS6YtSJ2DPHxcQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u8f6f\u4ef6\u4e0b\u8f7d<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4ecd\u7136\u4f7f\u7528\u6211\u4eec\u7684\u8001\u670b\u53cbminiconda\u4e0b\u8f7d\uff0c\u771f\u7684\u5f88\u65b9\u4fbf\uff0cminiconda\u7684\u5b89\u88c5\u65b9\u6cd5\u5c0f\u679c\u4e5f\u5206\u4eab\u8fc7\u54e6~<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">conda create --name fastp -y<\/span><\/code><code><span class=\"code-snippet_outer\">conda activate fastp<\/span><\/code><code><span class=\"code-snippet_outer\">conda install -c bioconda fastp<\/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;\"><\/span><\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.49899799599198397\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_I0yxHhatibSyerGWXaZhApQ3QF7o8g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAzUmbl9AKuU2I0OTXNMqJibibRxBlGvu7J0ZwEW56eQbIsRb82I0yxHhatibSyerGWXaZhApQ3QF7o8g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"499\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u6570\u636e\u5904\u7406<\/span><\/em><\/strong><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">##\u63d0\u53d6\u6587\u4ef6\u540d\u8f93\u51fa\u5230txt\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> file in `ls *_1.fastq.gz`; <span class=\"code-snippet__keyword\">do<\/span> <\/span><\/code><code><span class=\"code-snippet_outer\"> echo $(basename <span class=\"code-snippet__string\">\"$file\"<\/span>_1.fastq.gz | cut -f1 -d'_') >> sample.txt<\/span><\/code><code><span class=\"code-snippet_outer\">done <\/span><\/code><code><span class=\"code-snippet_outer\">#<span class=\"code-snippet__meta\">#fastp\u53bb\u63a5\u5934\u3001\u5220\u9664\u4f4e\u8d28\u91cfreads<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> sample in `cat sample.txt`; <span class=\"code-snippet__keyword\">do<\/span> <\/span><\/code><code><span class=\"code-snippet_outer\"> echo ${sample} | <\/span><\/code><code><span class=\"code-snippet_outer\"> fastp <\/span><\/code><code><span class=\"code-snippet_outer\"> --in1 \/media\/desk16\/iyun003\/GBS_test\/ERR_SRA\/${sample}_1.fastq.gz <\/span><\/code><code><span class=\"code-snippet_outer\"> --in2 \/media\/desk16\/iyun003\/GBS_test\/ERR_SRA\/${sample}_2.fastq.gz <\/span><\/code><code><span class=\"code-snippet_outer\"> --out1 \/media\/desk16\/iyun003\/GBS_test\/ERR_SRA\/${sample}_1_clean.fastq.gz <\/span><\/code><code><span class=\"code-snippet_outer\"> --out2 \/media\/desk16\/iyun003\/GBS_test\/ERR_SRA\/${sample}_2_clean.fastq.gz<\/span><\/code><code><span class=\"code-snippet_outer\">done<\/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;\">\u5728\u8fd9\u91cc\u53ef\u4ee5\u628a\u4e0a\u8ff0\u4ee3\u7801\u505a\u6210\u811a\u672c\u6765\u8fd0\u884c\u548c\u7ba1\u7406\u3002\u5176\u4e2din1\u8868\u793a\u8f93\u5165\u7684read1\u7684fastq\u6587\u4ef6out1\u8868\u793a\u8f93\u51fa\u7684\u8fc7\u6ee4\u540e\u7684read1\u7684clean reads.\u6ce8\u610f\u4fee\u6539\u4ee3\u7801\u4e2d\u7684\u8def\u5f84\u4e3a\u81ea\u5df1\u7684\u54e6~\u5c0f\u679c\u662f\u76f4\u63a5\u8fd0\u884c\u7684\u811a\u672c\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">nohup bash fastp.sh > fastq_log &<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6ca1\u6709\u610f\u5916\u7684\u8bdd\uff0c\u8ba9\u6211\u4eec\u6765\u770b\u770b\u7ed3\u679c\u5427\uff01\u4ee5\u4e0b\u5c31\u662f\u6211\u4eec\u5f97\u5230\u7684\u8fc7\u6ee4\u540e\u7684reads\u4e86\uff0c\u6210\u5c31\u611f\u6ee1\u6ee1\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\u4eca\u5929\u7684\u5185\u5bb9\u6682\u65f6\u5c31\u5230\u8fd9\u91cc\u4e86\uff0c\u6211\u4eec\u4e0b\u671f\u7ee7\u7eed\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: left;white-space: normal;\"><span style=\"font-size: 14px;\"><strong><em>\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f<\/em><\/strong><\/span><strong style=\"font-size: 14px;letter-spacing: 0.578px;\"><em>\u5b66 (biocloudservice.com)<\/em><\/strong><\/p>\n<p style=\"text-align: left;white-space: normal;\"><span style=\"font-size: 14px;\"><strong><em>\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<\/em><\/strong><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\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\/5_jEYQoRbKh3HUg3IGgzymibpTnmaM6Q.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><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/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=\"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>Fastp\u8f6f\u4ef6\uff1a\u5904\u7406fastq\u6587\u4ef6\u5b83\u8d85\u68d2\uff01 \u539f\u521b xg \u751f\u4fe1\u679c&n […]<\/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\/58998"}],"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=58998"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58998\/revisions"}],"predecessor-version":[{"id":59004,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58998\/revisions\/59004"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=58998"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=58998"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=58998"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":58998,"date":"2024-06-17T07:21:36","date_gmt":"2024-06-16T23:21:36","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58998"},"modified":"2024-06-17T07:21:36","modified_gmt":"2024-06-16T23:21:36","slug":"fastp%e8%bd%af%e4%bb%b6%ef%bc%9a%e5%a4%84%e7%90%86fastq%e6%96%87%e4%bb%b6%e5%ae%83%e8%b6%85%e6%a3%92%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58998","title":{"rendered":"Fastp\u8f6f\u4ef6\uff1a\u5904\u7406fastq\u6587\u4ef6\u5b83\u8d85\u68d2\uff01"},"content":{"rendered":"

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\n<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 60px}.rich_media_area_extra{padding:0 60px 21px 60px}}@media (min-width:1024px){.rich_media_area_primary_inner,.rich_media_area_extra_inner,body{max-width:677px;margin-left:auto;margin-right:auto}.rich_media_area_primary{padding-top:32px}}.rich_media{padding:20px;overflow:hidden;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}@media screen and (min-width:1024px){.rich_media_area_primary_inner,.rich_media_area_extra_inner{max-width:677px;margin-left:auto;margin-right:auto}.rich_media_area_primary{padding-top:32px}}.rich_media_content{overflow:hidden;color:#333;font-size:17px;word-wrap:break-word;-webkit-hyphens:auto;-ms-hyphens:auto;hyphens:auto;text-align:justify;position:relative;z-index:0}.rich_media_content *{max-width:100%!important;box-sizing:border-box!important;-webkit-box-sizing:border-box!important;word-wrap:break-word!important}.rich_media_content 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left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;width: 403.391px;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;\">\n<section style=\"margin-top: 10px;\">\n<section style=\"text-align: center;\">\n<section style=\"font-size: 16px;\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;vertical-align: top;width: 70.0348%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70.0348% !important;\">\n<section style=\"margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\"> \u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: 29.9652%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 29.9652% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;line-height: 0;\">\n<section>\n<section style=\"display: inline-block;vertical-align: middle;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 0;\">\n<section style=\"width: 111px;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1.75em;text-indent: 0em;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;height: auto;width: 111px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_GBhsibRAgNiaQsH4ichdP9ibEhHMFA-108.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyL6u7wJswOp8vtpzGp6vYngnlT6jiavu08Bvp2iblzGf3IkoBD9NGBhsibRAgNiaQsH4ichdP9ibEhHMFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"400\" style=\"vertical-align: middle;width: 100%;\" 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>\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 8px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"padding-left: 8px;display: inline-block;width: 578px;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;\">\n<p><span style=\"letter-spacing: 0.578px;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;\">fastp\u662f\u4e00\u6b3e\u7528\u4e8e\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6570\u636e\u8d28\u91cf\u63a7\u5236\u548c\u6570\u636e\u9884\u5904\u7406\u7684\u5feb\u901f\u5de5\u5177\u3002<\/span><\/span><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<section style=\"font-size: 16px;\">\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5b83\u53ef\u4ee5\u5bf9Illumina\u5e73\u53f0\u7684\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u3001\u8fc7\u6ee4\u4f4e\u8d28\u91cf\u5e8f\u5217\u3001\u622a\u65ad3’\u7aef\u4f4e\u8d28\u91cf\u5e8f\u5217\u3001\u53bb\u9664\u63a5\u5934\u5e8f\u5217\u7b49\u64cd\u4f5c\uff0c\u540c\u65f6\u8fd8\u53ef\u4ee5\u7edf\u8ba1\u5e8f\u5217\u8d28\u91cf\u5206\u5e03\u3001GC\u542b\u91cf\u5206\u5e03\u3001\u9519\u8bef\u7387\u5206\u5e03\u3001N\u542b\u91cf\u7b49\u4fe1\u606f\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;\">fastp\u91c7\u7528\u591a\u7ebf\u7a0b\u52a0\u901f\uff0c\u901f\u5ea6\u5feb\u3001\u51c6\u786e\u6027\u9ad8\uff0c\u5e76\u4e14\u652f\u6301\u591a\u79cd\u6570\u636e\u8f93\u5165\u548c\u8f93\u51fa\u683c\u5f0f\u3002\u4eca\u5929\u5c0f\u679c\u60f3\u5e26\u5927\u5bb6\u4e00\u8d77\u5b66\u4e60\u4e0b\u5982\u4f55\u7528fastp\u5bf9\u539f\u59cb\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u4e0b\u9762\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_fGErXbNqg62srzJVuGIw5CCF0DaBQg-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAzUmbl9AKuU2I0OTXNMqJibibG7LAuZZgjC83Ks5xTRdGYPsQfGErXbNqg62srzJVuGIw5CCF0DaBQg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u6570\u636e\u51c6\u5907<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5728ncbi\u7684sra\u6570\u636e\u5e93\u4e0b\u8f7d\u7684\u62df\u5357\u82a5\u6d4b\u5e8f\u6570\u636e\uff0c\u5305\u62ec\u56db\u4e2a\u57fa\u56e0\u578b\uff0c\u6bcf\u4e2a\u57fa\u56e0\u578b\u4e94\u4e2a\u91cd\u590d\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u94fe\u63a5\u5728\u8fd9\u91cc\uff0c\u5c0f\u679c\u4f7f\u7528\u7684\u6837\u672c\u7f16\u53f7\u4e3a<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">\uff08ERR9708198,ERR9708199,ERR9708200,ERR9708201,ERR9708202,ERR9708297,ERR9708298,ERR9708299,ERR9708300,ERR9708301,ERR9708388,ERR9708389,ERR9708390,ERR9708391,ERR9708392,ERR9708690,ERR9708691,ERR9708692,ERR9708693,ERR9708694\uff09<\/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;\">\u6570\u636e\u7684\u5177\u4f53\u4e0b\u8f7d\u65b9\u6cd5\u53ef\u4ee5\u67e5\u770b\u5f80\u671f\u5185\u5bb9\uff1a\u5c0f\u679c\u53d1\u73b0\u7528SRA Toolkit\u5de5\u5177\u4e0b\u8f7d\u8f6c\u5f55\u7ec4\u6570\u636e\u5f88\u597d\u7528\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd9\u91cc\u5c31\u4e0d\u518d\u8d58\u8ff0\u4e86\uff0c\u76f4\u63a5\u653e\u4ee3\u7801\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">nohup prefetch -O . $(<srr_acc_list.txt) &<=<span class=\"code-snippet__string\">\"\"<\/span> span=<span class=\"code-snippet__string\">\"\"<\/span>><\/span><\/code><code><span class=\"code-snippet_outer\">fastq-dump --gzip --split-files *.sra &<\/span><\/code><code><span class=\"code-snippet_outer\">gunzip *.fastq.gz<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\" powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"line-height: 0;text-align: center;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_gA7tHx97zkib2hlfDS6YtSJ2DPHxcQ-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAzUmbl9AKuU2I0OTXNMqJibibHmPicgof4fsMCDqBAdp8ByubHRgA7tHx97zkib2hlfDS6YtSJ2DPHxcQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u8f6f\u4ef6\u4e0b\u8f7d<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u4ecd\u7136\u4f7f\u7528\u6211\u4eec\u7684\u8001\u670b\u53cbminiconda\u4e0b\u8f7d\uff0c\u771f\u7684\u5f88\u65b9\u4fbf\uff0cminiconda\u7684\u5b89\u88c5\u65b9\u6cd5\u5c0f\u679c\u4e5f\u5206\u4eab\u8fc7\u54e6~<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">conda create --name fastp -y<\/span><\/code><code><span class=\"code-snippet_outer\">conda activate fastp<\/span><\/code><code><span class=\"code-snippet_outer\">conda install -c bioconda fastp<\/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;\"><\/span><\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.49899799599198397\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_I0yxHhatibSyerGWXaZhApQ3QF7o8g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAzUmbl9AKuU2I0OTXNMqJibibRxBlGvu7J0ZwEW56eQbIsRb82I0yxHhatibSyerGWXaZhApQ3QF7o8g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"499\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u6570\u636e\u5904\u7406<\/span><\/em><\/strong><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">##\u63d0\u53d6\u6587\u4ef6\u540d\u8f93\u51fa\u5230txt\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> file in `ls *_1.fastq.gz`; <span class=\"code-snippet__keyword\">do<\/span> <\/span><\/code><code><span class=\"code-snippet_outer\"> echo $(basename <span class=\"code-snippet__string\">\"$file\"<\/span>_1.fastq.gz | cut -f1 -d'_') >> sample.txt<\/span><\/code><code><span class=\"code-snippet_outer\">done <\/span><\/code><code><span class=\"code-snippet_outer\">#<span class=\"code-snippet__meta\">#fastp\u53bb\u63a5\u5934\u3001\u5220\u9664\u4f4e\u8d28\u91cfreads<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> sample in `cat sample.txt`; <span class=\"code-snippet__keyword\">do<\/span> <\/span><\/code><code><span class=\"code-snippet_outer\"> echo ${sample} | <\/span><\/code><code><span class=\"code-snippet_outer\"> fastp <\/span><\/code><code><span class=\"code-snippet_outer\"> --in1 \/media\/desk16\/iyun003\/GBS_test\/ERR_SRA\/${sample}_1.fastq.gz <\/span><\/code><code><span class=\"code-snippet_outer\"> --in2 \/media\/desk16\/iyun003\/GBS_test\/ERR_SRA\/${sample}_2.fastq.gz <\/span><\/code><code><span class=\"code-snippet_outer\"> --out1 \/media\/desk16\/iyun003\/GBS_test\/ERR_SRA\/${sample}_1_clean.fastq.gz <\/span><\/code><code><span class=\"code-snippet_outer\"> --out2 \/media\/desk16\/iyun003\/GBS_test\/ERR_SRA\/${sample}_2_clean.fastq.gz<\/span><\/code><code><span class=\"code-snippet_outer\">done<\/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;\">\u5728\u8fd9\u91cc\u53ef\u4ee5\u628a\u4e0a\u8ff0\u4ee3\u7801\u505a\u6210\u811a\u672c\u6765\u8fd0\u884c\u548c\u7ba1\u7406\u3002\u5176\u4e2din1\u8868\u793a\u8f93\u5165\u7684read1\u7684fastq\u6587\u4ef6out1\u8868\u793a\u8f93\u51fa\u7684\u8fc7\u6ee4\u540e\u7684read1\u7684clean reads.\u6ce8\u610f\u4fee\u6539\u4ee3\u7801\u4e2d\u7684\u8def\u5f84\u4e3a\u81ea\u5df1\u7684\u54e6~\u5c0f\u679c\u662f\u76f4\u63a5\u8fd0\u884c\u7684\u811a\u672c\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">nohup bash fastp.sh > fastq_log &<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6ca1\u6709\u610f\u5916\u7684\u8bdd\uff0c\u8ba9\u6211\u4eec\u6765\u770b\u770b\u7ed3\u679c\u5427\uff01\u4ee5\u4e0b\u5c31\u662f\u6211\u4eec\u5f97\u5230\u7684\u8fc7\u6ee4\u540e\u7684reads\u4e86\uff0c\u6210\u5c31\u611f\u6ee1\u6ee1\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\u4eca\u5929\u7684\u5185\u5bb9\u6682\u65f6\u5c31\u5230\u8fd9\u91cc\u4e86\uff0c\u6211\u4eec\u4e0b\u671f\u7ee7\u7eed\uff01<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: left;white-space: normal;\"><span style=\"font-size: 14px;\"><strong><em>\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f<\/em><\/strong><\/span><strong style=\"font-size: 14px;letter-spacing: 0.578px;\"><em>\u5b66 (biocloudservice.com)<\/em><\/strong><\/p>\n<p style=\"text-align: left;white-space: normal;\"><span style=\"font-size: 14px;\"><strong><em>\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<\/em><\/strong><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\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\/5_jEYQoRbKh3HUg3IGgzymibpTnmaM6Q.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><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/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=\"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>Fastp\u8f6f\u4ef6\uff1a\u5904\u7406fastq\u6587\u4ef6\u5b83\u8d85\u68d2\uff01 \u539f\u521b xg \u751f\u4fe1\u679c&n […]<\/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\/58998"}],"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=58998"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58998\/revisions"}],"predecessor-version":[{"id":59004,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58998\/revisions\/59004"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=58998"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=58998"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=58998"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}