{"id":66440,"date":"2026-11-14T19:10:11","date_gmt":"2026-11-14T11:10:11","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=66440"},"modified":"2026-11-14T19:21:21","modified_gmt":"2026-11-14T11:21:21","slug":"24-rnaseq-samples-server-deadline","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/24-rnaseq-samples-server-deadline\/","title":{"rendered":"24 \u4e2a RNA-seq \u6837\u672c\u600e\u6837\u53d8\u6210\u4e00\u5f20\u8868\u8fbe\u77e9\u9635\uff1f\u8bfb\u61c2 nf-core\/rnaseq"},"content":{"rendered":"
\n

\u5047\u5982\u6d4b\u5e8f\u516c\u53f8\u4ea4\u56de 24 \u4e2a\u6837\u672c\u7684 FASTQ\uff0c\u4f60\u60f3\u6bd4\u8f83\u5904\u7406\u7ec4\u548c\u5bf9\u7167\u7ec4\u3002\u6253\u5f00\u5176\u4e2d\u4e00\u4e2a\u6587\u4ef6\uff0c\u770b\u5230\u7684\u662f\u4e00\u6761\u6761\u6d4b\u5e8f\u8bfb\u6bb5\u3002\u5b83\u4eec\u5c5e\u4e8e\u54ea\u4e2a\u57fa\u56e0\uff1f\u6765\u81ea\u540c\u4e00\u4e2a\u57fa\u56e0\u7684\u51e0\u79cd\u8f6c\u5f55\u672c\uff0c\u8bfb\u6bb5\u8be5\u7b97\u7ed9\u8c01\uff1f\u540c\u4e00\u4e2a\u6837\u672c\u5206\u4e24\u6761 lane \u6d4b\u5e8f\uff0c\u6700\u540e\u5e94\u8be5\u5360\u8868\u8fbe\u77e9\u9635\u7684\u51e0\u5217\uff1f<\/p>\n

nf-core\/rnaseq \u8d1f\u8d23\u628a\u8fd9\u4e9b\u8bfb\u6bb5\u53d8\u6210\u6709\u6837\u672c\u540d\u3001\u6709\u57fa\u56e0\u540d\u3001\u80fd\u8ffd\u67e5\u6765\u6e90\u7684\u8868\u8fbe\u77e9\u9635\u3002<\/strong> \u8fd9\u4e2a GitHub \u4ed3\u5e93\u7528 Nextflow \u4e32\u8054\u8d28\u63a7\u3001\u6bd4\u5bf9\u3001\u5b9a\u91cf\u548c\u6c47\u603b\u3002\u4e0b\u9762\u4ee5 3.28.0 \u7248\u548c\u6709\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u53cc\u7aef bulk RNA-seq \u4e3a\u4f8b\uff0c\u6cbf\u7740\u4e00\u4e2a\u6837\u672c\u8d70\u4e00\u904d\u3002nf-core\/rnaseq \u4ed3\u5e93\u4e0e\u7248\u672c<\/a><\/p>\n

\"\u540c\u4e00\u57fa\u56e0\u7684\u957f\u77ed\u8f6c\u5f55\u672c\u5171\u4eab\u84dd\u8272\u5916\u663e\u5b50\uff0c\u53ea\u6709\u957f\u8f6c\u5f55\u672c\u542b\u6a59\u8272\u5916\u663e\u5b50\uff1b\u843d\u5728\u5171\u6709\u533a\u57df\u7684\u8bfb\u6bb5\u4e0d\u80fd\u72ec\u81ea\u533a\u5206\u4e24\u8005\u3002\"<\/p>\n

\u7b2c\u4e00\u5904\u5bb9\u6613\u51fa\u9519\u7684\u5730\u65b9\uff0c\u5728\u8fd0\u884c\u547d\u4ee4\u4e4b\u524d<\/h2>\n

\u5047\u8bbe\u4f9b\u4f53 A \u7684\u540c\u4e00\u6587\u5e93\u5206\u4e24\u6761 lane \u6d4b\u5e8f\uff0c\u4f9b\u4f53 B \u4e5f\u6d4b\u4e86\u4e00\u4e2a\u6587\u5e93\u3002\u5b83\u4eec\u5728\u6837\u672c\u8868\u91cc\u53ef\u4ee5\u8fd9\u6837\u5199\uff0c\u6587\u4ef6\u540d\u4ec5\u4f5c\u793a\u610f\u3002<\/p>\n

sample,fastq_1,fastq_2,strandedness,seq_platform\r\ndonorA,A_L1_R1.fastq.gz,A_L1_R2.fastq.gz,auto,ILLUMINA\r\ndonorA,A_L2_R1.fastq.gz,A_L2_R2.fastq.gz,auto,ILLUMINA\r\ndonorB,B_L1_R1.fastq.gz,B_L1_R2.fastq.gz,auto,ILLUMINA\r\n<\/code><\/pre>\n
\u8fd9\u4e09\u884c\u6700\u540e\u5e94\u5f97\u5230 \u4e24\u4e2a\u6837\u672c\u5217<\/strong>\u3002\u91cd\u590d\u7684 donorA<\/code> \u544a\u8bc9\u6d41\u7a0b\u628a\u540c\u4e00\u6837\u672c\u7684\u591a\u6b21\u6d4b\u5e8f\u5408\u5e76\u3002\u53cd\u8fc7\u6765\uff0c\u82e5\u628a\u6240\u6709\u5bf9\u7167\u7ec4\u6837\u672c\u90fd\u547d\u540d\u4e3a control<\/code>\uff0c\u72ec\u7acb\u751f\u7269\u5b66\u91cd\u590d\u4e5f\u53ef\u80fd\u88ab\u5408\u5e76\uff0c\u540e\u7eed\u5c31\u5931\u53bb\u4e86\u4f30\u8ba1\u7ec4\u5185\u53d8\u5f02\u7684\u4f9d\u636e\u3002\u9010\u4e00\u6838\u5bf9\u6837\u672c ID\u3001R1\/R2 \u914d\u5bf9\u548c\u4f9b\u4f53\u5bf9\u5e94\u5173\u7cfb\uff0c\u5f80\u5f80\u6bd4\u8c03\u6574\u6bd4\u5bf9\u53c2\u6570\u66f4\u503c\u5f97\u5148\u505a\u3002\u5206\u7ec4\u3001\u4f9b\u4f53\u3001\u6279\u6b21\u53e6\u5b58\u4e3a\u5b9e\u9a8c\u8bbe\u8ba1\u8868\uff0c\u540e\u9762\u505a\u7ec4\u95f4\u6bd4\u8f83\u65f6\u518d\u6309 ID \u5bf9\u4e0a\u3002\u5b98\u65b9\u6837\u672c\u8868\u4e0e\u591a\u6b21\u6d4b\u5e8f\u8bf4\u660e<\/a><\/p>\n
STAR \u5df2\u7ecf\u627e\u5230\u4f4d\u7f6e\uff0c\u4e3a\u4ec0\u4e48\u8fd8\u9700\u8981 Salmon\uff1f<\/h2>\n
\u60f3\u8c61\u4e00\u4e2a\u57fa\u56e0\u6709\u957f\u3001\u77ed\u4e24\u79cd\u8f6c\u5f55\u672c\uff0c\u4e24\u8005\u5171\u4eab\u4e00\u6bb5\u5916\u663e\u5b50\u3002\u4e00\u6761\u8bfb\u6bb5\u6070\u597d\u843d\u5728\u5171\u4eab\u533a\u57df\uff0cSTAR \u53ef\u4ee5\u628a\u5b83\u5b9a\u4f4d\u5230\u57fa\u56e0\u7ec4\u4e0a\u7684\u8fd9\u6bb5\u5916\u663e\u5b50\uff1b\u4ec5\u51ed\u8fd9\u6761\u8bfb\u6bb5\uff0c\u4ecd\u7136\u96be\u4ee5\u5224\u65ad\u5b83\u6765\u81ea\u957f\u8f6c\u5f55\u672c\u8fd8\u662f\u77ed\u8f6c\u5f55\u672c\u3002\u53e6\u4e00\u6761\u8bfb\u6bb5\u82e5\u8de8\u8fc7\u5176\u4e2d\u4e00\u79cd\u8f6c\u5f55\u672c\u7279\u6709\u7684\u526a\u63a5\u8fde\u63a5\uff0c\u5c31\u63d0\u4f9b\u4e86\u66f4\u6709\u533a\u5206\u529b\u7684\u8bc1\u636e\u3002<\/p>\n
\u5728\u9ed8\u8ba4\u7684 star_salmon<\/code> \u8def\u7ebf\u4e2d\uff0cSTAR \u505a\u526a\u63a5\u6bd4\u5bf9\uff0c\u5e76\u628a\u6bd4\u5bf9\u6295\u5c04\u5230\u8f6c\u5f55\u672c\u5750\u6807\u3002Salmon \u7efc\u5408\u7247\u6bb5\u4e0e\u5019\u9009\u8f6c\u5f55\u672c\u7684\u76f8\u5bb9\u5173\u7cfb\uff0c\u4f30\u8ba1\u5404\u8f6c\u5f55\u672c\u7684\u4e30\u5ea6\uff0c\u518d\u6c47\u603b\u5230\u57fa\u56e0\u5c42\u7ea7\u3002\u6240\u4ee5 Salmon \u7ed9\u51fa\u7684\u662f\u4f30\u8ba1\u8ba1\u6570\uff0c\u51fa\u73b0\u5c0f\u6570\u6709\u5176\u7edf\u8ba1\u542b\u4e49\u3002\u5982\u679c\u4e24\u4e2a\u8f6c\u5f55\u672c\u7684\u5927\u90e8\u5206\u5e8f\u5217\u76f8\u540c\uff0c\u57fa\u56e0\u603b\u91cf\u53ef\u4ee5\u76f8\u5bf9\u5bb9\u6613\u4f30\u8ba1\uff0c\u4e24\u79cd\u8f6c\u5f55\u672c\u5404\u5360\u591a\u5c11\u5374\u4ecd\u6709\u8f83\u5927\u4e0d\u786e\u5b9a\u6027\u3002\u6d41\u7a0b\u7684\u6bd4\u5bf9\u4e0e\u5b9a\u91cf\u9009\u9879<\/a> \u00b7 Salmon \u65b9\u6cd5\u8bba\u6587<\/a><\/p>\n
\u6253\u5f00\u7ed3\u679c\u76ee\u5f55\uff0c\u5148\u770b\u54ea\u51e0\u4e2a\u6587\u4ef6\uff1f<\/h2>\n
\n\n\n\n\n\n\n\n\n
\u624b\u5934\u7684\u95ee\u9898<\/th>\n\u6253\u5f00\u7684\u7ed3\u679c<\/th>\n\u600e\u4e48\u8bfb<\/th>\n<\/tr>\n<\/thead>\n
24 \u4e2a\u6837\u672c\u90fd\u5b9a\u91cf\u4e86\u5417\uff1f<\/td>\nsalmon.merged.gene_counts.tsv<\/code><\/td>\n\u57fa\u56e0\u5728\u884c\u3001\u6837\u672c\u5728\u5217\u3002\u5148\u628a\u6837\u672c\u5217\u540d\u4e0e\u8bbe\u8ba1\u8868\u9010\u4e00\u5339\u914d\uff0c\u518d\u770b\u5404\u5217\u7684\u8ba1\u6570\u91cf\u7ea7\u3002<\/td>\n<\/tr>\n
\u67d0\u4e2a\u57fa\u56e0\u5728\u8fd9\u4e2a\u6837\u672c\u91cc\u8868\u8fbe\u5f97\u591a\u5417\uff1f<\/td>\nsalmon.merged.gene_tpm.tsv<\/code><\/td>\nTPM \u540c\u65f6\u8003\u8651\u957f\u5ea6\u548c\u6837\u672c\u5185\u603b\u91cf\uff0c\u9002\u5408\u63cf\u8ff0\u76f8\u5bf9\u4e30\u5ea6\u3002\u505a DESeq2 \u7684\u7ec4\u95f4\u68c0\u9a8c\u65f6\uff0c\u5e94\u91c7\u7528\u5b83\u652f\u6301\u7684\u8ba1\u6570\u5bfc\u5165\u65b9\u5f0f\u3002<\/td>\n<\/tr>\n
\u67d0\u4e2a\u6837\u672c\u4e3a\u4f55\u663e\u5f97\u5f02\u5e38\uff1f<\/td>\nMultiQC \u62a5\u544a\u3001\u5bf9\u5e94\u6837\u672c\u7684 STAR \u65e5\u5fd7<\/td>\n\u67e5\u770b\u6bd4\u5bf9\u3001\u6d4b\u5e8f\u8d28\u91cf\u548c\u94fe\u7279\u5f02\u6027\u7b49\u6307\u6807\u3002\u53ea\u6709\u4e00\u4e2a\u6837\u672c\u5f02\u5e38\u65f6\uff0c\u4f18\u5148\u6838\u5bf9\u8be5\u6837\u672c\uff1b\u6574\u6279\u90fd\u4f4e\u65f6\uff0c\u56de\u5934\u67e5\u7269\u79cd\u3001\u53c2\u8003\u7248\u672c\u548c\u5efa\u5e93\u4fe1\u606f\u3002<\/td>\n<\/tr>\n
\u51c6\u5907\u505a\u5dee\u5f02\u8868\u8fbe\uff0c\u600e\u6837\u4fdd\u7559\u5b9a\u91cf\u4fe1\u606f\uff1f<\/td>\n\u5404\u6837\u672c\u7684 quant.sf<\/code><\/td>\n\u4e00\u6761\u5e38\u7528\u9014\u5f84\u662f\u6309\u540c\u7248\u6ce8\u91ca\u5efa\u7acb\u8f6c\u5f55\u672c\u5230\u57fa\u56e0\u7684\u6620\u5c04\uff0c\u7528 tximport \u6c47\u603b\uff0c\u518d\u7528 DESeq2 \u7684 DESeqDataSetFromTximport<\/code> \u63a5\u5165\u8bbe\u8ba1\u8868\u3002<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u4e00\u4e2a\u503c\u5f97\u8ffd\u67e5\u7684\u7ec4\u5408\u662f\uff1a\u8bfb\u6bb5\u80fd\u6bd4\u5bf9\u4e0a\u53c2\u8003\u57fa\u56e0\u7ec4\uff0c\u843d\u5165\u9884\u671f\u6ce8\u91ca\u6216\u53c2\u4e0e\u5b9a\u91cf\u7684\u6bd4\u4f8b\u5374\u504f\u4f4e<\/strong>\u3002\u5148\u67e5 FASTA \u548c GTF \u662f\u5426\u5bf9\u5e94\u540c\u4e00\u7ec4\u88c5\u3001\u67d3\u8272\u4f53\u547d\u540d\u662f\u5426\u4e00\u81f4\uff0c\u518d\u770b\u94fe\u7279\u5f02\u6027\u5224\u65ad\u548c\u6587\u5e93\u7c7b\u578b\u3002\u6bd4\u5bf9\u6210\u529f\u53ea\u80fd\u8bf4\u660e\u627e\u5230\u4e86\u76f8\u5bb9\u7684\u4f4d\u7f6e\uff0c\u4e0d\u80fd\u4fdd\u8bc1\u73b0\u6709\u6ce8\u91ca\u5b8c\u6574\u8986\u76d6\u90a3\u4e9b\u4f4d\u7f6e\u3002\u8fd9\u4e5f\u89e3\u91ca\u4e86\u4e3a\u4ec0\u4e48\u591a\u770b\u4e24\u4efd\u8f93\u51fa\u6bd4\u76ef\u4f4f\u4e00\u4e2a\u201c\u6bd4\u5bf9\u7387\u201d\u66f4\u6709\u610f\u4e49\u3002\u5b98\u65b9\u8f93\u51fa\u6587\u4ef6\u53ca\u5dee\u5f02\u8868\u8fbe\u5bfc\u5165\u8bf4\u660e<\/a><\/p>\n
\u600e\u6837\u5f00\u59cb\uff0c\u53c8\u8be5\u5728\u54ea\u4e00\u6b65\u505c\u4e0b\u6765\u6838\u5bf9\uff1f<\/h2>\n
\u5df2\u7ecf\u88c5\u597d\u517c\u5bb9\u7684 Nextflow \u548c Docker\uff0c\u5e76\u80fd\u62c9\u53d6\u5bb9\u5668\u65f6\uff0c\u53ef\u4ee5\u5148\u8fd0\u884c\u4ed3\u5e93\u7684\u5c0f\u6d4b\u8bd5\u3002\u4e0b\u9762\u56fa\u5b9a\u7248\u672c\uff0c\u65b9\u4fbf\u65e5\u540e\u590d\u73b0\u3002<\/p>\n
nextflow run nf-core\/rnaseq -r 3.28.0 -profile test,docker --outdir results_test\r\n<\/code><\/pre>\n
\u5c0f\u6d4b\u8bd5\u7528\u6765\u68c0\u67e5\u73af\u5883\u80fd\u5426\u628a\u6d41\u7a0b\u8d70\u901a\u3002\u6362\u6210\u81ea\u5df1\u7684\u9879\u76ee\uff0c\u8fd8\u8981\u63d0\u4f9b\u6837\u672c\u8868\u3001\u5339\u914d\u7684\u53c2\u8003 FASTA \u548c GTF\uff0c\u5e76\u7528\u4ee3\u8868\u6027\u5b8c\u6574\u6587\u5e93\u786e\u8ba4\u8f93\u51fa\u3002\u8fd9\u4e2a\u6d41\u7a0b\u89e3\u51b3\u4e86\u4e0a\u6e38\u5904\u7406\u53e3\u5f84\u7684\u4e00\u81f4\u6027\uff0c\u5b9e\u9a8c\u8bbe\u8ba1\u4ecd\u7531\u7814\u7a76\u8005\u8d1f\u8d23<\/strong>\u3002\u5982\u679c\u5904\u7406\u7ec4\u5168\u5728\u4e00\u6279\u5efa\u5e93\u3001\u5bf9\u7167\u7ec4\u5168\u5728\u53e6\u4e00\u6279\uff0c\u8868\u8fbe\u77e9\u9635\u518d\u6574\u9f50\uff0c\u4e5f\u65e0\u6cd5\u5355\u51ed\u8fd9\u6279\u6570\u636e\u5206\u6e05\u5904\u7406\u6548\u5e94\u548c\u6279\u6b21\u6548\u5e94\u3002\u5355\u7ec6\u80de\u6761\u5f62\u7801\u3001UMI \u548c\u7ec6\u80de\u5c42\u9762\u7684\u8d28\u63a7\u4e5f\u9700\u8981\u9488\u5bf9\u76f8\u5e94\u5b9e\u9a8c\u8bbe\u8ba1\u9009\u62e9\u6d41\u7a0b\u3002\u7248\u672c\u8bf4\u660e\u4e0e\u6d4b\u8bd5\u5165\u53e3<\/a><\/p>\n
\u4ece\u4e00\u4e2a\u6837\u672c\u6269\u5927\u5230 24 \u4e2a\u65f6\uff0c\u518d\u8c08\u670d\u52a1\u5668<\/h2>\n
\u5148\u62ff\u4e00\u4e2a\u6570\u636e\u91cf\u5c45\u4e2d\u7684\u6587\u5e93\u548c\u4e00\u4e2a\u504f\u5927\u7684\u6587\u5e93\uff0c\u7528\u6700\u7ec8\u53c2\u8003\u8dd1\u5b8c\u540c\u4e00\u8def\u7ebf\u3002\u8bb0\u5f55 STAR \u7684\u5cf0\u503c\u5185\u5b58\u3001\u6392\u5e8f\u671f\u95f4\u5de5\u4f5c\u76d8\u7684\u6700\u4f4e\u5269\u4f59\u7a7a\u95f4\uff0c\u4ee5\u53ca\u4ece\u8bfb\u5165\u5230\u5b9a\u91cf\u5b8c\u6210\u7528\u4e86\u591a\u4e45\u3002\u968f\u540e\u8ba9\u591a\u4e2a\u6837\u672c\u540c\u65f6\u8dd1\uff0c\u6309\u6574\u4e2a\u6279\u6b21\u5b9e\u9645\u5b8c\u6210\u7684\u6837\u672c\u6570 \u00f7 \u7ecf\u8fc7\u7684\u5c0f\u65f6\u6570<\/strong>\u8ba1\u7b97\u541e\u5410\u91cf\u3002\u82e5\u52a0\u5e76\u53d1\u540e\u541e\u5410\u51e0\u4e4e\u4e0d\u53d8\uff0c\u53bb\u770b\u6392\u5e8f\u8bfb\u5199\u548c\u4efb\u52a1\u7b49\u5f85\uff1b\u7ee7\u7eed\u52a0\u7ebf\u7a0b\u53ef\u80fd\u53ea\u4f1a\u8ba9\u66f4\u591a\u4efb\u52a1\u4e00\u8d77\u7b49\u3002Nextflow \u6267\u884c\u62a5\u544a\u4e0e\u65f6\u95f4\u7ebf<\/a><\/p>\n
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