{"id":393,"date":"2022-10-02T10:50:15","date_gmt":"2022-10-02T02:50:15","guid":{"rendered":"http:\/\/xn--805-6f0f4a6598f.fun\/?p=393"},"modified":"2024-05-22T16:04:14","modified_gmt":"2024-05-22T08:04:14","slug":"393","status":"publish","type":"post","link":"https:\/\/stu.chcmu.asia\/index.php\/2022\/10\/02\/393\/","title":{"rendered":"SRA Toolkit\u4e0b\u8f7d\u4e0e\u5b89\u88c5"},"content":{"rendered":"<h4>\u7b2c\u4e00\u6b65\uff1a\u8fdb\u5165NCBI\u9009\u62e9\u201cDownload\u201d, \u8fdb\u5165\u540e\u9009\u62e9\u201cDownload Tools\u201d\u5de5\u5177\u4e0b\u8f7d<\/h4>\n<p><img decoding=\"async\" src=\"https:\/\/img-blog.csdnimg.cn\/20200914093032773.png?x-oss-process=image\/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3dlaXhpbl80Mzg0MDU3Ng==,size_16,color_FFFFFF,t_70#pic_center\" alt=\"\" \/><br \/>\n<img decoding=\"async\" src=\"https:\/\/img-blog.csdnimg.cn\/20200914093127465.png?x-oss-process=image\/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3dlaXhpbl80Mzg0MDU3Ng==,size_16,color_FFFFFF,t_70#pic_center\" alt=\"\" \/><\/p>\n<h4>\u7b2c\u4e8c\u6b65\uff1a\u9009\u62e9\u201cSRA Toolkit\u201d\u7684\u201cDownload\u201d\u6309\u94ae\uff0c\u8fdb\u5165\u7248\u672c\u9009\u62e9<\/h4>\n<p>\u6b64\u5904\u6211\u9009\u62e9\u7684\u662f\u201cCentOS Linux 64 bit architecture\u201d\uff0c\u82e5\u60f3\u5728linux\u7cfb\u7edf\u4e2d\u4e0b\u8f7d\uff0c\u53ef\u9009\u62e9\u53f3\u952e\u201c\u590d\u5236\u94fe\u63a5\u5730\u5740\u201d\uff0c\u7136\u540e\u5230 Linux \u7cfb\u7edf\u4e2d\u7528 wget \u547d\u4ee4\u83b7\u53d6\u3002<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/img-blog.csdnimg.cn\/20200914093236279.png?x-oss-process=image\/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3dlaXhpbl80Mzg0MDU3Ng==,size_16,color_FFFFFF,t_70#pic_center\" alt=\"\" \/><br \/>\n<img decoding=\"async\" src=\"https:\/\/img-blog.csdnimg.cn\/2020091409333268.png?x-oss-process=image\/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3dlaXhpbl80Mzg0MDU3Ng==,size_16,color_FFFFFF,t_70#pic_center\" alt=\"\" \/><\/p>\n<p>\u4e0b\u8f7d sratoolkit \u6587\u4ef6\uff0c\u5f53\u524d\u7248\u672c\u4e3a3.0\uff1a<\/p>\n<pre><code class=\"language-bash\">wget https:\/\/ftp-trace.ncbi.nlm.nih.gov\/sra\/sdk\/3.0.0\/sratoolkit.3.0.0-centos_linux64.tar.gz<\/code><\/pre>\n<h4>\u7b2c\u4e09\u6b65\uff1a\u5b89\u88c5\u4e0e\u4f7f\u7528<\/h4>\n<p>\u6b64\u5b89\u88c5\u5305\u89e3\u538b\u5373\u53ef\u4f7f\u7528\uff0c\u4f46\u9700\u5148\u914d\u7f6e\u5b58\u50a8\u4f4d\u7f6e\u3002<\/p>\n<pre><code class=\"language-bash\">tar zxvf sratoolkit.3.0.0-centos_linux64.tar.gz\ncd sratoolkit.3.0.0-centos_linux64\/bin\nvdb-config -i # \u914d\u7f6e\u5b58\u50a8\u4f4d\u7f6e<\/code><\/pre>\n<p>\u4f7f\u7528\u65b9\u6cd5\uff1a<\/p>\n<pre><code class=\"language-bash\">prefetch SRR1036346  # SRR1036346\u4e3a\u4f60\u60f3\u8981\u83b7\u53d6\u7684 sra \u6570\u636e\u7f16\u53f7\n# fastq_dump \u53ef\u5c06 sra \u6570\u636e\u8f6c\u5316\u4e3a fastq \u683c\u5f0f\u6570\u636e\nfastq-dump --split-3 --gzip SRR1036346.sra\n# fasterq_dump \u652f\u6301\u591a\u7ebf\u7a0b\uff0c\u66f4\u5feb\u901f\nfasterq-dump --split-3 .\/SRR1036346.sra -e 16 -o .\/SRR1036346\n# \u82e5\u4e3a\u53cc\u7aef\u6570\u636e\uff0c\u5219\u4f1a\u4ea7\u751f\u4e24\u4e2a\u6570\u636e\uff0c\u5206\u522b\u4e3aSRR1036346_1.fastq \u548c SRR1036346_2.fastq\uff1b\u82e5\u4e3a\u5355\u7aef\u6570\u636e\uff0c\u5219\u53ea\u6709\u4e00\u4e2a\u6570\u636e\uff0c\u4e3aSRR1036346.fastq\n# 10X \u6570\u636e\u9700\u6dfb\u52a0 --include-technical \u751f\u6210\u4e09\u4e2a\u6587\u4ef6\nfasterq-dump --split-files --include-technical ..\/SRR7722941.sra\n# \u5e76\u884c\u8fd0\u7b97\nconda install -c bioconda parallel-fastq-dump\nparallel-fastq-dump -t 16  -O .\/ --split-files --gzip -s SRR7722941.sra<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u7b2c\u4e00\u6b65\uff1a\u8fdb\u5165NCBI\u9009\u62e9\u201cDownload\u201d, \u8fdb\u5165\u540e\u9009\u62e9\u201cDownload Tools\u201d\u5de5\u5177\u4e0b\u8f7d \u7b2c\u4e8c\u6b65\uff1a\u9009 [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[6,30],"tags":[],"class_list":["post-393","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","category-biosoft"],"_links":{"self":[{"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/posts\/393","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/comments?post=393"}],"version-history":[{"count":1,"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/posts\/393\/revisions"}],"predecessor-version":[{"id":1642,"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/posts\/393\/revisions\/1642"}],"wp:attachment":[{"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/media?parent=393"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/categories?post=393"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/stu.chcmu.asia\/index.php\/wp-json\/wp\/v2\/tags?post=393"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}