{"id":2232,"date":"2025-10-17T19:27:19","date_gmt":"2025-10-17T11:27:19","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=2232"},"modified":"2025-10-17T19:46:30","modified_gmt":"2025-10-17T11:46:30","slug":"nf-core-rnaseq%e8%bf%9b%e8%a1%8c%e8%bd%ac%e5%bd%95%e7%bb%84%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/10\/17\/nf-core-rnaseq%e8%bf%9b%e8%a1%8c%e8%bd%ac%e5%bd%95%e7%bb%84%e5%88%86%e6%9e%90\/","title":{"rendered":"nf-core\/rnaseq\u8fdb\u884c\u8f6c\u5f55\u7ec4\u5206\u6790"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"2232\" class=\"elementor elementor-2232\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-304d453 e-flex e-con-boxed e-con e-parent\" data-id=\"304d453\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-fb40674 elementor-widget elementor-widget-heading\" data-id=\"fb40674\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">1. \u524d\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b925673 elementor-widget elementor-widget-text-editor\" data-id=\"b925673\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u62ff\u5230\u8f6c\u5f55\u7ec4\u7684\u6d4b\u5e8f\u6570\u636e\uff0c\u600e\u4e48\u5f97\u5230\u57fa\u56e0\u7ec4\u4e2d\u6bcf\u4e2a\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\u5462\uff1f\u6b63\u5e38\u8981\u7ecf\u5386\u201c\u6307\u63a7-\u6bd4\u5bf9-\u5b9a\u91cf-\u6807\u51c6\u5316\u201d\u6d41\u7a0b\uff0c\u624d\u80fd\u5f97\u5230\u8868\u8fbe\u91cf\u3002\u800cnf-core\/rnaseq\u5c31\u662f\u5e2e\u52a9\u6211\u4eec\u4e00\u6761\u547d\u4ee4\u5b8c\u6210\u4e0a\u8ff0\u6b65\u9aa4\uff0c\u76f4\u63a5\u5f97\u5230\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u4e00\u4e2a\u57fa\u4e8eNextflow\u5199\u7684pipline\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-34cc6d5 elementor-widget elementor-widget-heading\" data-id=\"34cc6d5\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">2. \u4e0b\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a405163 elementor-widget elementor-widget-text-editor\" data-id=\"a405163\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>nf-core\u7c7b\u4f3c\u4e8e\u4e00\u4e2a\u5de5\u5177\u7bb1\uff0c\u4e0b\u9762\u4f1a\u6709\u5f88\u591a\u5de5\u5177\uff0crnaseq\u5c31\u662f\u5176\u4e2d\u4e00\u4e2a\uff0c\u6240\u4ee5\u8981\u5148\u4e0b\u8f7dnf-core\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9ba8cf4 elementor-widget elementor-widget-code-highlight\" data-id=\"9ba8cf4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>mamba creaye -n nf-core\nmamba install bioconda::nf-core<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6d8c08e elementor-widget elementor-widget-text-editor\" data-id=\"6d8c08e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u63a5\u4e0b\u6765\uff0c\u901a\u8fc7nf-core\u4e0b\u8f7drnaseq<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1f12caa elementor-widget elementor-widget-code-highlight\" data-id=\"1f12caa\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>nf-core download nf-core\/rnaseq<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3858b16 elementor-widget elementor-widget-text-editor\" data-id=\"3858b16\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u4f9d\u6b21\u9009\u62e9\uff0cdev\uff0cnone\uff0ctar.gz\uff0c\u5b8c\u6210\u540e\u4f1a\u51fa\u73b0\u4e86\u4e00\u4e2a\u201cnf-core-rnaseq_dev\u201d\uff0c\u91cc\u9762\u5c31\u662fnf-core\/rnaseq\u8f6f\u4ef6\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-89e44a9 elementor-widget elementor-widget-image\" data-id=\"89e44a9\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"877\" height=\"331\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/\u5fae\u4fe1\u56fe\u7247_2025-10-17_193631_077.png\" class=\"attachment-large size-large wp-image-2238\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/\u5fae\u4fe1\u56fe\u7247_2025-10-17_193631_077.png 877w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/\u5fae\u4fe1\u56fe\u7247_2025-10-17_193631_077-300x113.png 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/\u5fae\u4fe1\u56fe\u7247_2025-10-17_193631_077-768x290.png 768w\" sizes=\"(max-width: 877px) 100vw, 877px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b488919 elementor-widget elementor-widget-heading\" data-id=\"b488919\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3. \u8fd0\u884c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5e152dc elementor-widget elementor-widget-code-highlight\" data-id=\"5e152dc\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>nextflow run ~\/Software\/nf-core\/nf-core-rnaseq_dev\/dev\/ --input sample.csv  --gff ..\/Anno\/Final_result\/Prunus_pedunculata_Chr.gff --fasta ..\/Anno\/Final_result\/Prunus_pedunculata_Chr.fasta --outdir RNA-seq_seticuspe -profile docker\n\n# --input sample.csv: \u6307\u5b9a\u8f93\u5165\u7684\u6837\u672c\u4fe1\u606f\u6587\u4ef6\uff08samplesheet\uff09\u3002\u8fd9\u4e2a CSV \u6587\u4ef6\u901a\u5e38\u5305\u542b\u591a\u5217\uff0c\u5982\u6837\u672cID\u3001FASTQ\u6587\u4ef6\u7684\u8def\u5f84\uff08\u5355\u7aef\u6216\u53cc\u7aef R1\/R2\uff09\u3001\u5206\u7ec4\u4fe1\u606f\u7b49\uff0c\u6d41\u7a0b\u4f1a\u6839\u636e\u8fd9\u4e2a\u6587\u4ef6\u6765\u5904\u7406\u6bcf\u4e2a\u6837\u672c\u3002\n# --gff ..\/Anno\/Final_result\/Prunus_pedunculata_Chr.gff: \u6307\u5b9a\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6\uff0c\u683c\u5f0f\u4e3a GFF\u3002\u8fd9\u4e2a\u6587\u4ef6\u5305\u542b\u4e86\u57fa\u56e0\u3001\u8f6c\u5f55\u672c\u3001\u5916\u663e\u5b50\u7b49\u5728\u57fa\u56e0\u7ec4\u4e0a\u7684\u4f4d\u7f6e\u4fe1\u606f\uff0c\u662f\u8fdb\u884c\u57fa\u56e0\u8868\u8fbe\u5b9a\u91cf\u6240\u5fc5\u9700\u7684\u3002\n# --fasta ..\/Anno\/Final_result\/Prunus_pedunculata_Chr.fasta: \u6307\u5b9a\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u5e8f\u5217\u6587\u4ef6\uff0c\u683c\u5f0f\u4e3a FASTA\u3002RNA-seq \u7684\u8bfb\u957f\uff08reads\uff09\u5c06\u4f1a\u6bd4\u5bf9\u5230\u8fd9\u4e2a\u53c2\u8003\u57fa\u56e0\u7ec4\u4e0a\u3002\n# --outdir RNA-seq_seticuspe: \u6307\u5b9a\u6240\u6709\u5206\u6790\u7ed3\u679c\u7684\u8f93\u51fa\u76ee\u5f55\u3002\u6d41\u7a0b\u8fd0\u884c\u7ed3\u675f\u540e\uff0c\u6240\u6709\u7684\u62a5\u544a\u3001\u6bd4\u5bf9\u6587\u4ef6\u3001\u5b9a\u91cf\u7ed3\u679c\u7b49\u90fd\u4f1a\u4fdd\u5b58\u5728\u8fd9\u4e2a\u540d\u4e3a RNA-seq_seticuspe \u7684\u6587\u4ef6\u5939\u4e2d\u3002\n# -profile docker: \u6307\u5b9a\u8fd0\u884c\u6240\u4f7f\u7528\u7684\u914d\u7f6e profile\u3002docker \u662f\u4e00\u4e2a\u9884\u8bbe\u7684 profile\uff0c\u5b83\u544a\u8bc9 Nextflow \u4f7f\u7528 Docker \u5bb9\u5668\u6765\u8fd0\u884c\u6d41\u7a0b\u4e2d\u7684\u6bcf\u4e00\u4e2a\u5206\u6790\u6b65\u9aa4\uff08\u5982 STAR \u6bd4\u5bf9, Salmon \n  \u5b9a\u91cf\u7b49\uff09\u3002\u8fd9\u6837\u505a\u7684\u597d\u5904\u662f\uff0c\u6240\u6709\u8f6f\u4ef6\u53ca\u5176\u4f9d\u8d56\u90fd\u6253\u5305\u5728\u5bb9\u5668\u4e2d\uff0c\u786e\u4fdd\u4e86\u5206\u6790\u73af\u5883\u7684\u4e00\u81f4\u6027\u548c\u53ef\u91cd\u590d\u6027\uff0c\u907f\u514d\u4e86\u624b\u52a8\u5b89\u88c5\u5927\u91cf\u8f6f\u4ef6\u7684\u9ebb\u70e6\u3002\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b6df453 elementor-widget elementor-widget-text-editor\" data-id=\"b6df453\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd9\u91cc\u8981\u5f3a\u8c03\u7684\u662f\uff0c\u8981\u624b\u52a8\u6574\u7406\u4e00\u4e2asample.csv\u6587\u4ef6\uff0c\u8bb0\u5f55\u4e86\u6837\u672c\u7684\u6d4b\u5e8f\u6587\u4ef6\u7684\u8def\u5f84\u548c\u4fe1\u606f\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9af64df elementor-widget elementor-widget-code-highlight\" data-id=\"9af64df\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>sample,fastq_1,fastq_2,strandedness\nSRR18362927,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR18362927_1.fastq.gz,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR18362927_2.fastq.gz,auto\nSRR18362928,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR18362928_1.fastq.gz,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR18362928_2.fastq.gz,auto\nSRR18362929,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR18362929_1.fastq.gz,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR18362929_2.fastq.gz,auto\nSRR30835667,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR30835667_1.fastq.gz,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR30835667_2.fastq.gz,auto\nSRR30835668,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR30835668_1.fastq.gz,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR30835668_2.fastq.gz,auto\nSRR30835669,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR30835669_1.fastq.gz,\/home\/majunpeng\/sda2\/Pangenome_Catus\/Hpchic_readjujst\/Straned\/Catus\/Total_vcf\/SV_RNA-seq\/RNA-seq\/Chrysanthemum_indicum\/SRR30835669_2.fastq.gz,auto<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c2f997b elementor-widget elementor-widget-heading\" data-id=\"c2f997b\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">4. \u8f93\u51fa\u7ed3\u679c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-655649e elementor-widget elementor-widget-text-editor\" data-id=\"655649e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div 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