{"id":25276,"date":"2024-01-19T17:03:03","date_gmt":"2024-01-19T09:03:03","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25276"},"modified":"2024-01-19T17:03:04","modified_gmt":"2024-01-19T09:03:04","slug":"%e4%b8%80%e5%88%86%e9%92%9f%e5%ae%8c%e6%88%90fastq%e6%96%87%e4%bb%b6%e8%b4%a8%e9%87%8f%e8%af%84%e4%bc%b0","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25276","title":{"rendered":"\u4e00\u5206\u949f\u5b8c\u6210FASTQ\u6587\u4ef6\u8d28\u91cf\u8bc4\u4f30"},"content":{"rendered":"<p>\u4e0a\u4e00\u6b21\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e86\u5982\u4f55\u5904\u7406FASTQ\u6587\u4ef6\uff0c\u76f8\u4fe1\u806a\u660e\u7684\u5c0f\u4f19\u4f34\u4eec\u5df2\u7ecf\u8f7b\u677e\u638c\u63e1\uff0c\u5bf9\u4e0b\u4e00\u9636\u6bb5\u7684\u8c03\u6574\u8dc3\u8dc3\u6b32\u8bd5\u5566\u3002\u6b63\u5982\u4e0a\u4e00\u6b21\u6240\u8bf4\uff0c\u6570\u636e\u8d28\u91cf\u8bc4\u4f30\u548c\u9884\u5904\u7406\u6b65\u9aa4\u5728\u4f7f\u7528FASTQ\u6587\u4ef6\u8fdb\u884c\u8fdb\u4e00\u6b65\u5206\u6790\u4e4b\u524d\u662f\u5f88\u91cd\u8981\u7684\uff0c\u90a3\u4e48\u8fd9\u4e00\u6b21\u5c0f\u679c\u5c31\u6765\u7ed9\u5927\u5bb6\u5206\u4eab\u5982\u4f55\u5728\u4e00\u5206\u949f\u5185\u8f7b\u677e\u5b8c\u6210FASTQ\u6587\u4ef6\u8d28\u91cf\u8bc4\u4f30\uff0c\u5e76\u5bf9\u8d28\u91cf\u8bc4\u4f30\u7ed3\u679c\u9644\u4e0a\u8be6\u7ec6\u7684\u8bf4\u660e\uff0c\u5e72\u8d27\u6ee1\u6ee1\uff0c\u5c0f\u4f19\u4f34\u4eec\u5feb\u6765\u770b\u770b\u5427\u3002<\/p>\n<h2>\u4e3a\u4ec0\u4e48\u8981\u8fdb\u884c\u8d28\u91cf\u8bc4\u4f30\u548c\u9884\u5904\u7406\uff1f<\/h2>\n<ol>\n<li>\u9519\u8bef\u8bc6\u522b\u548c\u4fee\u6b63\uff1aFASTQ\u6587\u4ef6\u5305\u542b\u4e86\u6d4b\u5e8f\u5b9e\u9a8c\u751f\u6210\u7684\u539f\u59cb\u78b1\u57fa\u5e8f\u5217\u53ca\u5176\u5bf9\u5e94\u7684\u8d28\u91cf\u503c\u3002\u8fd9\u4e9b\u8d28\u91cf\u503c\u53cd\u6620\u4e86\u6bcf\u4e2a\u78b1\u57fa\u6d4b\u5e8f\u7684\u53ef\u4fe1\u5ea6\u3002<strong>\u6570\u636e\u8d28\u91cf\u8bc4\u4f30\u53ef\u4ee5\u5e2e\u52a9\u8bc6\u522b\u548c\u4fee\u6b63\u53ef\u80fd\u5b58\u5728\u7684\u6d4b\u5e8f\u9519\u8bef<\/strong>\uff0c\u4f8b\u5982\u6d4b\u5e8f\u78b1\u57fa\u66ff\u4ee3\u3001\u63d2\u5165\u6216\u5220\u9664\u9519\u8bef\u3002\u901a\u8fc7\u4fee\u590d\u8fd9\u4e9b\u9519\u8bef\uff0c\u53ef\u4ee5\u63d0\u9ad8\u540e\u7eed\u5206\u6790\u7684\u51c6\u786e\u6027\u3002<\/li>\n<li>\u5197\u4f59\u548c\u4f4e\u8d28\u91cf\u7247\u6bb5\u8fc7\u6ee4\uff1aFASTQ\u6587\u4ef6\u901a\u5e38\u5305\u542b\u5927\u91cf\u7684\u6d4b\u5e8f\u7247\u6bb5\uff0c\u5176\u4e2d\u53ef\u80fd\u5b58\u5728\u5197\u4f59\u5e8f\u5217\u3001PCR\u91cd\u590d\u6216\u8005\u4f4e\u8d28\u91cf\u7684\u7247\u6bb5\u3002\u5bf9\u6570\u636e\u8fdb\u884c\u8d28\u91cf\u8bc4\u4f30\u548c\u9884\u5904\u7406\u53ef\u4ee5<strong>\u8fc7\u6ee4\u6389\u8fd9\u4e9b\u4e0d\u5fc5\u8981\u7684\u7247\u6bb5\uff0c\u51cf\u5c11\u6570\u636e\u91cf\u548c\u566a\u97f3<\/strong>\uff0c\u63d0\u9ad8\u540e\u7eed\u5206\u6790\u7684\u6548\u7387\u548c\u51c6\u786e\u6027\u3002<\/li>\n<li>\u8d28\u91cf\u63a7\u5236\uff1a\u6570\u636e\u8d28\u91cf\u8bc4\u4f30\u53ef\u4ee5\u63d0\u4f9b\u5173\u4e8e\u6d4b\u5e8f\u6570\u636e\u8d28\u91cf\u7684\u8be6\u7ec6\u7edf\u8ba1\u4fe1\u606f\uff0c\u4f8b\u5982\u6bcf\u4e2a\u78b1\u57fa\u7684\u8d28\u91cf\u5206\u5e03\u3001\u6d4b\u5e8f\u6df1\u5ea6\u7b49\u3002<strong>\u8fd9\u4e9b\u4fe1\u606f\u5bf9\u4e8e\u9009\u62e9\u5408\u9002\u7684\u9608\u503c\u3001\u786e\u5b9a\u5206\u6790\u65b9\u6cd5\u548c\u89e3\u91ca\u7ed3\u679c\u975e\u5e38\u91cd\u8981\u3002<\/strong>\u901a\u8fc7\u5bf9\u6570\u636e\u8d28\u91cf\u8fdb\u884c\u63a7\u5236\uff0c\u53ef\u4ee5\u786e\u4fdd\u540e\u7eed\u5206\u6790\u7684\u53ef\u9760\u6027\u548c\u53ef\u91cd\u590d\u6027\u3002<\/li>\n<li>\u6570\u636e\u6e05\u6d17\uff1a\u5728\u8fdb\u884c\u67d0\u4e9b\u5206\u6790\u4e4b\u524d\uff0c\u9700\u8981\u5bf9\u6570\u636e\u8fdb\u884c\u6e05\u6d17\uff0c\u4ee5<strong>\u53bb\u9664\u4f4e\u8d28\u91cf\u7684\u78b1\u57fa\u6216\u8005\u4e0d\u53ef\u9760\u7684\u7247\u6bb5\u3002<\/strong>\u8fd9\u6837\u53ef\u4ee5\u6392\u9664\u566a\u97f3\u5f15\u5165\u548c\u504f\u5dee\uff0c\u786e\u4fdd\u5206\u6790\u7ed3\u679c\u66f4\u52a0\u51c6\u786e\u548c\u53ef\u9760\u3002<\/li>\n<\/ol>\n<h2>FASTQ\u6570\u636e\u8d28\u63a7\u8fc7\u6ee4\u8f6f\u4ef6\u2014SOAPnuke<\/h2>\n<p>\u5f53\u4eca\u5e02\u9762\u4e0a\u6709\u8bb8\u591a\u53ef\u4ee5\u5bf9FASTQ\u6570\u636e\u8fdb\u884c\u8d28\u63a7\u8fc7\u6ee4\u7684\u8f6f\u4ef6\uff0cSOAPnuke\u662f\u5176\u4e2d\u5bf9\u65b0\u624b\u6bd4\u8f83\u53cb\u597d\uff0c\u4f7f\u7528\u8d77\u6765\u6bd4\u8f83\u7b80\u5355\u7684\u5165\u95e8\u7ea7\u8f6f\u4ef6\u3002\u5c0f\u679c\u8fd9\u6b21\u5c31\u5728linux\u4e2d\u4ee5SOAPnuke\u4e3a\u4f8b\uff0c\u6559\u7ed9\u5927\u5bb6\u8d28\u91cf\u8bc4\u4f30\u7684\u6b65\u9aa4\u3002<\/p>\n<p>\u4e0b\u9762\u662fSOAPnuke\u7684\u4e00\u4e9b\u5e38\u7528\u53c2\u6570\u7684\u4ecb\u7ecd\uff1a<\/p>\n<ol>\n<li>-1\uff1a\u6307\u5b9a\u5f85\u5904\u7406\u6570\u636e\u7684\u7b2c\u4e00\u5bf9\uff08\u6216\u552f\u4e00\uff09\u6d4b\u5e8f\u6587\u4ef6\u7684\u8def\u5f84\u3002<\/li>\n<li>-2\uff1a\u6307\u5b9a\u5f85\u5904\u7406\u6570\u636e\u7684\u7b2c\u4e8c\u5bf9\u6d4b\u5e8f\u6587\u4ef6\u7684\u8def\u5f84\uff08\u5982\u679c\u662f\u53cc\u7aef\u6d4b\u5e8f\u6570\u636e\uff09\u3002<\/li>\n<li>-r\uff1a\u6307\u5b9a\u4fdd\u5b58\u5904\u7406\u7ed3\u679c\u7684\u8def\u5f84\u3002<\/li>\n<li>-C\uff1a\u7528\u4e8e\u6307\u5b9a\u914d\u7f6e\u6587\u4ef6\u7684\u8def\u5f84\u3002\u914d\u7f6e\u6587\u4ef6\u5305\u542b\u4e86SOAPnuke\u7684\u8be6\u7ec6\u8bbe\u7f6e\uff0c\u5982\u5904\u7406\u8fc7\u7a0b\u4e2d\u6240\u4f7f\u7528\u7684\u8d28\u91cf\u8ba1\u7b97\u65b9\u6cd5\u3001\u8d28\u91cf\u9608\u503c\u7b49\u3002\u53ef\u4ee5\u6839\u636e\u9700\u8981\u8fdb\u884c\u81ea\u5b9a\u4e49\u8bbe\u7f6e\u3002<\/li>\n<li>-5\uff1a\u6307\u5b9a5&#8217;\u7aef\u526a\u5207\u7684\u78b1\u57fa\u6570\u3002\u8be5\u53c2\u6570\u7528\u4e8e\u53bb\u9664\u6d4b\u5e8f\u6587\u5e93\u4e2d\u7684\u4f4e\u8d28\u91cf\u672b\u7aef\uff0c\u63d0\u9ad8\u6570\u636e\u8d28\u91cf\u3002<\/li>\n<li>-3\uff1a\u6307\u5b9a3&#8217;\u7aef\u526a\u5207\u7684\u78b1\u57fa\u6570\u3002\u8be5\u53c2\u6570\u540c\u6837\u7528\u4e8e\u53bb\u9664\u6d4b\u5e8f\u6587\u5e93\u4e2d\u7684\u4f4e\u8d28\u91cf\u672b\u7aef\u3002<\/li>\n<li>-l\uff1a\u6307\u5b9a\u6700\u77ed\u6709\u6548\u8bfb\u957f\uff08clean read length\uff09\u3002\u8be5\u53c2\u6570\u7528\u4e8e\u53bb\u9664\u8f83\u77ed\u7684reads\uff0c\u63d0\u9ad8\u6570\u636e\u8d28\u91cf\u3002<\/li>\n<li>-q\uff1a\u6307\u5b9a\u8d28\u91cf\u9608\u503c\u3002\u8be5\u53c2\u6570\u7528\u4e8e\u5c06\u4f4e\u4e8e\u6307\u5b9a\u8d28\u91cf\u9608\u503c\u7684\u78b1\u57fa\u6807\u8bb0\u4e3aN\uff0c\u4ece\u800c\u53bb\u9664\u4f4e\u8d28\u91cf\u7684\u78b1\u57fa\u3002<\/li>\n<li>-n\uff1a\u6307\u5b9a\u5141\u8bb8\u7684\u6700\u5927\u8fde\u7eed\u4f4e\u8d28\u91cf\u78b1\u57fa\u6570\u3002\u8be5\u53c2\u6570\u7528\u4e8e\u53bb\u9664\u5177\u6709\u8fde\u7eed\u4f4e\u8d28\u91cf\u78b1\u57fa\u7684reads\u3002<\/li>\n<li>-M\uff1a\u6307\u5b9a\u4fdd\u7559\u7684\u6700\u5c0f\u5e73\u5747\u8d28\u91cf\u503c\u3002\u8be5\u53c2\u6570\u7528\u4e8e\u8fc7\u6ee4\u6389\u5e73\u5747\u8d28\u91cf\u4f4e\u4e8e\u6307\u5b9a\u9608\u503c\u7684reads\u3002<\/li>\n<li>-d\uff1a\u6307\u5b9aadapter\u5e8f\u5217\u6587\u4ef6\u7684\u8def\u5f84\u3002\u8be5\u53c2\u6570\u7528\u4e8e\u53bb\u9664reads\u4e2d\u7684adapter\u5e8f\u5217\u3002<\/li>\n<li>-t\uff1a\u6307\u5b9a\u7ebf\u7a0b\u6570\u3002\u8be5\u53c2\u6570\u7528\u4e8e\u6307\u5b9a\u5e76\u884c\u5904\u7406\u7684\u7ebf\u7a0b\u6570\uff0c\u52a0\u5feb\u5904\u7406\u901f\u5ea6\u3002<\/li>\n<li>-D\uff1a\u5f00\u542fadapter\u5e8f\u5217\u7684\u5b58\u5728\u6027\u68c0\u6d4b\u548c\u53bb\u9664\u3002<\/li>\n<li>-I\uff1a\u5f00\u542fPCR\u5197\u4f59\u5e8f\u5217\u7684\u68c0\u6d4b\u548c\u53bb\u9664\u3002<\/li>\n<li>-O\uff1a\u5f00\u542fPCR\u5197\u4f59\u5e8f\u5217\u914d\u5bf9\u6bd4\u5bf9\u7684\u68c0\u6d4b\u548c\u53bb\u9664\u3002<\/li>\n<\/ol>\n<p>\u8fd9\u4e9b\u53ea\u662fSOAPnuke\u7684\u4e00\u4e9b\u5e38\u7528\u53c2\u6570\uff0c\u8fd8\u6709\u5176\u4ed6\u4e00\u4e9b\u53ef\u9009\u53c2\u6570\u7528\u4e8e\u66f4\u8be6\u7ec6\u5730\u63a7\u5236\u9884\u5904\u7406\u8fc7\u7a0b\u3002\u4f7f\u7528\u9002\u5f53\u7684\u53c2\u6570\u8bbe\u7f6e\u53ef\u4ee5\u6839\u636e\u5b9e\u9645\u9700\u6c42\u8fdb\u884c\u6570\u636e\u8d28\u91cf\u63a7\u5236\u548c\u9884\u5904\u7406\uff0c\u63d0\u9ad8\u540e\u7eed\u5206\u6790\u7684\u51c6\u786e\u6027\u548c\u53ef\u9760\u6027\u3002\u5c0f\u4f19\u4f34\u4eec\u5982\u679c\u60f3\u4e86\u89e3\u7684\u8bdd\u53ef\u4ee5\u5728\u547d\u4ee4\u884c\u4e2d\u8fd0\u884cSOAPnuke filter \u2013help\uff0c\u67e5\u770bSOAPnuke\u66f4\u591a\u5b8c\u6574\u53c2\u6570\u3002<\/p>\n<h2>\u64cd\u4f5c\u6b65\u9aa4<\/h2>\n<p># \u521b\u5efa\u6587\u4ef6\u5939<br \/>\nmkdir 00_ref 01_clean 02_align 03_SNPCalling 04_annotation raw_data<\/p>\n<p>\u4e4b\u6240\u4ee5\u521b\u5efa\u8fd9\u4e48\u591a\u6587\u4ef6\u5939\u662f\u56e0\u4e3a\u8d28\u91cf\u8bc4\u4f30\u53ea\u662f\u6211\u4eec\u5206\u6790\u6d41\u7a0b\u7684\u7b2c\u4e00\u6b65\uff0c\u5728\u540e\u7eed\u5206\u6790\u6d41\u7a0b\u8fd8\u4f1a\u4ea7\u751f\u4ee5\u4e0b\u6587\u4ef6\uff1a<\/p>\n<p>\u8fc7\u6ee4\u2192clean.fq\u2192\u6bd4\u5bf9\u2192clean.bwa.sam\u2192\u6570\u636e\u683c\u5f0f\u8f6c\u6362\u2192clean.bwa.bam\u2192\u7d22\u5f15\u7ed3\u679c\u6392\u5e8f\u2192clean.bwa.sorted.bam\u2192\u53d8\u5f02\u68c0\u6d4b\u2192clean.bwa.snp.vcf<\/p>\n<p>\u8fd9\u91cc\u5c0f\u679c\u5efa\u8bae\u5927\u5bb6\u4f7f\u7528mobaXterm\u6765\u8fde\u63a5linux\u670d\u52a1\u5668\uff0c\u56e0\u4e3amobaXterm\u53ef\u4ee5\u76f4\u63a5\u5728\u547d\u4ee4\u884c\u7a97\u53e3\u5de6\u8fb9\u5de5\u5177\u680f\u5b9e\u73b0\u6570\u636e\u7684\u4e0a\u4f20\u548c\u4e0b\u8f7d\u7b49\u529f\u80fd\uff0c\u975e\u5e38\u7b80\u5355\u65b9\u4fbf\uff0c\u5982\u4e0b\u56fe\u8fd9\u4e2a\u6846\u4e2d\u7684\u7bad\u5934\u5c31\u662f\u6570\u636e\u4e0a\u4f20\u6309\u94ae\uff0c\u800c\u5b83\u5de6\u8fb9\u53e6\u4e00\u4e2a\u7bad\u5934\u5c31\u662f\u6570\u636e\u4e0b\u8f7d\u6309\u94ae\u3002\u521b\u5efa\u6210\u529f\u540e\u901a\u8fc7\u5de6\u4fa7\u5de5\u5177\u680f\u5c06\u4e0b\u673a\u6570\u636e\u62f7\u8d1d\u81f3\u65b0\u5efa\u76ee\u5f55raw_data\uff1a<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"99\" class=\"wp-image-25279\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-25276-1.png?resize=640%2C99\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-25276-1.png?w=846 846w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-25276-1.png?resize=300%2C46 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-25276-1.png?resize=768%2C119 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-25276-1.png?resize=600%2C93 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p># \u4f7f\u7528SOAPnuke\u8fc7\u6ee4\u6570\u636e\uff08\u6ce8\u610f\uff0c\u6b64\u547d\u4ee4\u4e3a\u8fde\u7eed\u4e00\u884c\uff09<br \/>\nSOAPnuke filter -1 .\/raw_data\/G1211112269_Barcode_e.fq.gz -l 10 -q 0.5 -n 0.01 -T 1 -o .\/01_clean\/ -C test_clean.fq.gz<br \/>\n# \u53ef\u572801_clean\u8def\u5f84\u4e0b\u4f7f\u7528less\u547d\u4ee4\u9010\u4e00\u67e5\u770b\u6d4b\u5e8f\u6570\u636e\u8d28\u91cf\u8bc4\u4f30\u8868\uff0c\u7b80\u5355\u5c55\u793a\u8fc7\u6ee4\u524d\u540e\u6570\u636e\u603b\u4f53\u60c5\u51b5\u5982\u4e0b<br \/>\nless 01_clean\/Basic_Statistics_of_Sequencing_Quality.txt<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"255\" class=\"wp-image-25280\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-25276-2.png?resize=640%2C255\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-25276-2.png?w=1067 1067w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-25276-2.png?resize=300%2C119 300w, 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href=\"http:\/\/www.biocloudservice.com\/home.html\">http:\/\/www.biocloudservice.com\/home.html<\/a>\uff0c\u5927\u5bb6\u5728\u65b0\u63a5\u89e6\u4e00\u4e2a\u77e5\u8bc6\u7684\u65f6\u5019\uff0c\u4e0e\u5176\u5148\u82b1\u8d39\u5927\u91cf\u65f6\u95f4\u6b7b\u5543\u77e5\u8bc6\u70b9\uff0c\u4e0d\u5982\u5148\u5229\u7528\u597d\u5de5\u5177\u5148\u81ea\u5df1\u4e0a\u624b\u63a5\u89e6\u6d41\u7a0b\uff0c\u5728\u8dd1\u5b8c\u4e00\u904d\u5168\u6d41\u7a0b\u540e\u518d\u8fd4\u56de\u53bb\u7406\u89e3\u77e5\u8bc6\u70b9\uff0c\u76f8\u4fe1\u53ef\u4ee5\u66f4\u597d\u66f4\u5feb\u5730\u7406\u89e3\uff0c\u8fbe\u5230\u4e8b\u534a\u529f\u500d\u7684\u6548\u679c\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u4e0a\u4e00\u6b21\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e86\u5982\u4f55\u5904\u7406FASTQ\u6587\u4ef6\uff0c\u76f8\u4fe1\u806a\u660e\u7684\u5c0f\u4f19\u4f34\u4eec\u5df2\u7ecf\u8f7b\u677e\u638c\u63e1\uff0c\u5bf9\u4e0b\u4e00\u9636\u6bb5\u7684\u8c03\u6574\u8dc3\u8dc3\u6b32\u8bd5\u5566\u3002\u6b63\u5982 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