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14px;\">\u5728\u8fdb\u884c\u5176\u5b83\u5206\u6790\u4e4b\u524d\uff0c\u6211\u4eec\u901a\u5e38\u5b66\u5bf9\u8f6c\u5f55\u672c\u548c\u57fa\u56e0\u7684\u4e30\u5ea6\u8fdb\u884c\u5b9a\u91cf\u3002\u5728Trinity\u4e2d\u63d0\u4f9b\u4e86\u8c03\u7528\u4e09\u79cd\u4e0d\u540c\u8f6f\u4ef6\u7684\u811a\u672c\uff0cRSEM\uff0ckallisto\u548csalmon\u3002\u503c\u5f97\u6ce8\u610f\u7684\u662fTrinity\u5e76\u6ca1\u6709\u540c\u65f6\u6253\u5305\u5b89\u88c5\u597d\u8fd9\u4e09\u4e2a\u8f6f\u4ef6\uff0c\u9700\u8981\u6211\u4eec\u81ea\u5df1\u4e0b\u8f7d\u5e76\u914d\u7f6e\u597d\u76f8\u5bf9\u5e94\u7684\u73af\u5883\u53d8\u91cf\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u4f7f\u7528\u4e00\u4e0b\u9762\u7684\u811a\u672cperl\u811a\u672c\u8fdb\u884c\u8ba1\u7b97<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<h2 style=\"text-align: center;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><o:p><\/o:p><\/span><\/h2>\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=\"shell\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/util\/align_and_estimate_abundance.pl<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e3b\u8981\u53c2\u6570\u5982\u4e0b\uff1a<\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code><span class=\"code-snippet_outer\"># --transcripts <string>: \u8f6c\u5f55\u672c\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"># --seqType <string>: fq|fa<\/span><\/code><code><span class=\"code-snippet_outer\"># \u82e5\u4e3apaired-end\u6570\u636e\uff1a--left <string>: \u5de6\u7aefreads\u6587\u4ef6 --right <string>: \u53f3\u7aefreads\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"># single-end\u6570\u636e\uff1a--single <string>: \u539f\u59cbreads\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"># --est_method <string>: RSEM|kallisto|salmon<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u6bd4\u5982\u8bf4\u6211\u4eecRSEM\u6765\u8fdb\u884c\u5b9a\u91cf\uff0c\u76f8\u5173\u547d\u4ee4\u5982\u4e0b\uff1a<o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\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=\"swift\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/util\/align_and_estimate_abundance.pl --transcript Trinity.fasta --est_method RSEM --aln_method bowtie --seqType fq --left reads_1.fq --right reads_2.fq --trinity_mode --prep_reference --output_dir rsem_outdir<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e4b\u540e\u4f1a\u8fd4\u8fd8\u4e24\u4e2a\u8f93\u51fa\u6587\u4ef6\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><br \/><\/span><\/p>\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=\"css\"><code><span class=\"code-snippet_outer\">\u2019RSEM.isoforms.results\u2019\u3001\u2019RSEM.genes.results\u2019<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u57fa\u56e0\u5206\u578b\u7684\u7ed3\u679c\u5982\u4e0b\u6240\u793a\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.32416787264833574\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_tDAzLUAhLdibIVrEEzqdK6XTvwgicg-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecdL2vlkV15jZeBgYRQKK1ZWsl72mtDAzLUAhLdibIVrEEzqdK6XTvwgicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"691\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e86\u4e00\u4e2a\u8f6c\u5f55\u672c\uff0c\u8bb0\u5f55\u4e86\u8f6c\u5f55\u672c\u7684\u957f\u5ea6\uff0c\u6709\u6548\u957f\u5ea6\uff0c\u671f\u671b\u6570\u91cf\uff0cTPM\u548cFPKM\uff0c\u53ef\u4ee5\u770b\u5230\u7b2c\u4e8c\u884c\u8fd9\u4e2a\u57fa\u56e0\u6709\u7740\u6700\u9ad8\u7684\u8868\u8fbe\u91cf\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u81f3\u6b64\uff0c\u6211\u4eec\u53ef\u4ee5\u5bf9\u6bcf\u4e2a\u6837\u672c\u6784\u5efa\u8f6c\u5f55\u672c\u548c\u57fa\u56e0\u7684\u8868\u8fbe\u77e9\u9635\uff0c\u4f7f\u7528\u4e0b\u9762\u8fd9\u4e2a\u811a\u672c\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><br \/><\/p>\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=\"objectivec\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/util\/abundance_estimates_to_matrix.pl<\/span><\/code><code><span class=\"code-snippet_outer\"># --est_method <string>: RSEM|kallisto|salmon<\/span><\/code><code><span class=\"code-snippet_outer\"># --gene_trans_map <string>: \u57fa\u56e0\u548c\u8f6c\u5f55\u672c\u7684\u8f6c\u6362\u6587\u4ef6<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4f8b\u5b50\u5982\u4e0b\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\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=\"shell\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/util\/abundance_estimates_to_matrix.pl --est_method RSEM --gene_trans_map Trinity.fasta.gene_trans_map --name_sample_by_basedir<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u4f1a\u5f97\u5230\u4ee5\u4e0b\u4e09\u4e2a\u6587\u4ef6\uff1a<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018RSEM.isoform.count.matrix\u2019: \u539f\u59cbcounts\u6570\u636e<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018RSEM.isoform.TPM.not_cross_norm\u2019: TPM\u8868\u8fbe\u91cf\uff08\u6ca1\u6709\u8fdb\u884c\u8de8\u6837\u672c\u5f52\u4e00\u5316\uff09<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018RSEM.isoform.TMM.EXPR.matrix\u2019: TMM\u5f52\u4e00\u5316\u7684\u8868\u8fbe\u503c<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 20px;\"><em><strong>2.\u5dee\u5f02\u8868\u8fbe\u5206\u6790<\/strong><\/em><\/span><strong><span style=\"font-family: \u7b49\u7ebf;font-size: 12pt;background: rgb(255, 255, 0);\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"font-size: 14px;font-family: Optima-Regular, PingFangTC-light;\">\u5f97\u5230\u4e86\u8868\u8fbe\u77e9\u9635\u4e4b\u540e\u6211\u4eec\u5c31\u53ef\u4ee5\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u4e86\uff0cTrinity\u4e2d\u4f7f\u7528\u7684\u662fEdgeR\u8fd9\u4e2aR\u5305\u6765\u505a\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u540c\u6837\u9700\u8981\u54b1\u4eec\u7684\u7cfb\u7edf\u4e2d\u88c5\u6709\u76f8\u5bf9\u5e94\u7684R\u73af\u5883\u548c\u8f6f\u4ef6\u5305\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: Optima-Regular, PingFangTC-light;\">\u5177\u4f53\u811a\u672c\u547d\u4ee4\u548c\u53c2\u6570\u5982\u4e0b\u6240\u793a\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/Analysis\/DifferentialExpression\/run_DE_analysis.pl<\/span><\/code><code><span class=\"code-snippet_outer\"># --matrix|m <string>: \u539f\u59cbcount\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\"># --method <string>: edgeR|DESeq2|voom<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u8fd0\u884c\u4ee5\u4e0b\u811a\u672c\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\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=\"shell\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/Analysis\/DifferentialExpression\/run_DE_analysis.pl --matrix RSEM.isoform.count.matrix --method edgeR \u2013samples_file samples_described.txt<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5173\u4e8eedgeR\u7684\u53c2\u6570\u8bbe\u7f6e\u53ef\u4ee5\u67e5\u8be2<\/span><span style=\"color: rgb(5, 99, 193);text-decoration: underline;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">edgeR manual<\/span><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u7136\u540e\u6211\u4eec\u4f1a\u5f97\u5230\u4e09\u4e2a\u6587\u4ef6\uff0c\u5206\u522b\u662f\uff1a<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018${prefix}.sampleA_vs_sampleB.${method}.DE_results\u2019<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018${prefix}.sampleA_vs_sampleB.${method}.MA_n_Volcano.pdf\u2019<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">${prefix}.sampleA_vs_sampleB.${method}.Rscript\u2019<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770bDE_results\u6587\u4ef6\u7684\u5934\u51e0\u884c\uff0c\u8bb0\u5f55\u7740log fold change\u548c\u76f8\u5bf9\u5e94\u7684\u7edf\u8ba1\u91cf\uff08Pvalue\uff0cFDR\u77eb\u6b63\uff09<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7734487734487735\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ric7Roia2TLQ9m7HMffibgXs1v8LDA-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecd1S1CKbs51fjXCSYvUVjPAialaKeWric7Roia2TLQ9m7HMffibgXs1v8LDA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u540c\u65f6\u8fd8\u6709\u706b\u5c71\u56fe<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.46320346320346323\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_TgtOC9s2G7EaUJ2Eicug4YjnkasicA-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecdFiauVu7OST9alKm1E752jdurbkZTgtOC9s2G7EaUJ2Eicug4YjnkasicA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u5bf9\u4e8e\u5dee\u5f02<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u8868\u8fbe<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u7b49\u7ebf;\">\u7684\u4e00\u4e2a\u6bd4\u8f83\u521d\u59cb\u7684\u5206\u6790\u5c31\u662f\u53bb\u83b7\u53d6\u90a3\u4e9b\u524d\u540e\u8868\u8fbe\u5dee\u5f02\u6781\u5927\u7684\u8f6c\u5f55\u672c\uff08\u6700\u663e\u8457\u7684<\/span><span style=\"font-family:\u7b49\u7ebf;\">FDR\u548cfold<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">–<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">change\uff09\uff0c<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u7136\u540e\u6839\u636e\u4e0d\u540c\u7684\u8868\u8fbe\u6a21\u5f0f\u5c06\u8fd9\u4e9b\u8f6c\u5f55\u672c\u5212\u5206\u805a\u7c7b\u3002\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u811a\u672c\u8fdb\u884c\u805a\u7c7b<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/Analysis\/DifferentialExpression\/analyze_diff_expr.pl <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> --matrix <string>: TMM.EXPR.matrix<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> -P <<span class=\"code-snippet__built_in\">float<\/span>>: pvalue\u9608\u503c<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> -C <<span class=\"code-snippet__built_in\">float<\/span>>: \u6700\u5c0f\u7684fold change\u6570<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5982\u5c0f\u679c\u4e0b\u9762\u4e3e\u7684\u4f8b\u5b50\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/Analysis\/DifferentialExpression\/analyze_diff_expr.pl --matrix ..\/Trinity_trans.TMM .EXPR.matrix -P 1e-3 -C 2<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;\"><span style=\"font-size: 14px;font-family: \u7b49\u7ebf;\">\u7136\u540e\u6211\u4eec\u5c31\u80fd\u5f97\u5230\u5982\u4e0b\u5dee\u5f02\u57fa\u56e0\u548c\u4e0d\u540c\u6837\u672c\u7684\u70ed\u56fe\uff1a<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 12pt;\"><o:p><\/o:p><\/span><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1.092485549132948\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_tqjcst3WBZq7fWGiboR6REqicZxS9A-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecdxmh22XEKN8EjGaEbgqSXqIaDestqjcst3WBZq7fWGiboR6REqicZxS9A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 20px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><em><strong><span style=\"font-size: 20px;font-weight: bold;\"><br \/><\/span><\/strong><\/em><\/span><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 20px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><em><strong><span style=\"font-size: 20px;font-weight: bold;\">3.<\/span><span style=\"font-size: 20px;\">\u8f6c\u5f55\u672c\u529f\u80fd\u6ce8\u91ca<\/span><\/strong><\/em><\/span><strong><span style=\"font-family: \u7b49\u7ebf;font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"font-size: 14px;\"><span style=\"font-size: 14px;font-family: \u7b49\u7ebf;\"><\/span><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5728\u6211\u4eec\u5f97\u5230\u4e86\u62fc\u63a5\u7684\u8f6c\u5f55\u672c\u4ee5\u53ca\u76f8\u5e94\u7684\u57fa\u56e0\u96c6\u4e4b\u540e\uff0c\u6211\u4eec\u81ea\u7136\u800c\u7136\u60f3\u77e5\u9053\u8fd9\u4e9b\u57fa\u56e0\u5bcc\u96c6\u5728\u4ec0\u4e48\u6837\u7684\u529f\u80fd\u4e0a\u3002\u540c\u6837\u7684\uff0c\u54b1\u4eec\u5f3a\u5927\u7684Trinity\u63d0\u4f9b\u4e86\u4e00\u5957\u5b8c\u6574\u7684\u6d41\u7a0b\u3002\u9996\u5148\u6211\u4eec\u901a\u8fc7\u4ee5\u4e0b\u811a\u672c\u6765\u83b7\u53d6\u6bcf\u4e2a\u57fa\u56e0\u6240\u5bf9\u5e94\u7684GO term\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\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=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/util\/extract_GO_assignments_from_Trinotate_xls.pl --Trinoate_xls trinotate.xls -G --include_ancestral_terms > go_annotations.txt<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u7136\u540e\u6211\u4eec\u518d\u4f7f\u7528Bioconductor\u4e2d\u7684\u5305GOseq\u8fdb\u884c\u529f\u80fd\u5bcc\u96c6\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/Analysis\/DifferentialExpression\/run_GOseq.pl --factor_labeling factor_labeling.txt --GO_assignments go_annotations.txt --lengths gene.lengths.txt<\/span><\/code><\/pre>\n<\/section>\n<p style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;text-align: left;text-wrap: wrap;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5176\u4e2d\u2019factor_labeling.txt\u2019\u8fd9\u4e2a\u6587\u4ef6\u8bb0\u8f7d\u7740\u4e0d\u540c\u6837\u672c\u95f4\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u96c6\uff0c\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.170767004341534\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_aH8yqPaLHqNEaVUFGUeTHxyFWYicQA-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecdNC0l3I5htlN7EKNbDykeGx8ibLiaH8yqPaLHqNEaVUFGUeTHxyFWYicQA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"691\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u800c\u5bf9\u4e8e\u2018gene.lengths.txt\u2019\u8fd9\u4e2a\u6587\u4ef6\uff0c\u6211\u4eec\u4f7f\u7528\u5982\u4e0b\u547d\u4ee4\u8fdb\u884c\u521b\u5efa\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;text-align: left;text-wrap: wrap;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/util\/misc\/fasta_seq_length.pl Trinity.fasta > Trinity.fasta.seq_lengths<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/util\/misc\/TPM_weighted_gene_length.py --gene_trans_map trinity_out_dir\/Trinity.fasta.gene_trans_map --trans_lengths Trinity.fasta.seq_lens --TPM_matrix isoforms.TMM.EXPR.matrix > Trinity.gene_lengths.txt<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5728\u6700\u540e\u6211\u4eec\u5c31\u4f1a\u5f97\u5230\u4e00\u4e2a\u5982\u4e0b\u7684\u56fe\u6807\uff0c\u5176\u4e2d\u8bb0\u5f55\u7740\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u5bcc\u96c6\u5230\u7684\u529f\u80fd\u901a\u8def\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:Consolas;mso-fareast-font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';color:rgb(51,51,51);font-size:10.5000pt;mso-font-kerning:1.0000pt;background:rgb(238,239,240);mso-shading:rgb(238,239,240);\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.15050651230101303\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_mUKEvcLoBgokUicmEO4TfubUzsdUbw-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecd5LkZ9LUU4Jl1aj2NBDBAiba2stmUKEvcLoBgokUicmEO4TfubUzsdUbw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"691\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4ee5\u4e0a\u5c31\u662f\u4f7f\u7528Trinity\u8fdb\u884cde novo\u8f6c\u5f55\u672c\u62fc\u63a5\u3001\u4e0b\u6e38\u5206\u6790\u7684\u5168\u90e8\u5185\u5bb9\uff0c\u5982\u679c\u4f60\u6709\u4ec0\u4e48\u95ee\u9898\u7684\u8bdd\u6b22\u8fce\u548c\u5c0f\u679c\u8ba8\u8bba\uff01<\/span><span style=\"text-align: center;letter-spacing: 0.034em;\"><\/span><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\u4e3a\uff1a(http:\/\/www.biocloudservice.com\/home.html)\uff0c\u5176\u4e2d\u4e5f\u5305\u62ec\u4e86\u901a\u8def\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/313\/313.php)\uff0c\u5355\u7ec6\u80de\u7684\u57fa\u56e0\u5171\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/906\/906.php)\u7b49\u5404\u79cd\u5c0f\u5de5\u5177\u54e6~\uff0c\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u767b\u5f55\u7f51\u7ad9\u8fdb\u884c\u4e86\u89e3\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\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 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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<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;caret-color: red;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;text-align: left;letter-spacing: 0.034em;font-size: 14px;\">\u5728\u4e0a\u4e00\u671f\u7684\u6559\u5b66\u4e2d\u5c0f\u679c\u8bb2\u5230\u4e86\u5982\u4f55\u4e0b\u8f7d\u548c\u4f7f\u7528Trinity\u7ec4\u88c5\u8f6c\u5f55\u672c\uff0c\u5e76\u4e14\u8bc4\u4f30\u8f6c\u5f55\u672c\u7684\u8d28\u91cf\uff0c\u5728\u672c\u671f\u4e2d\u6211\u4eec\u5c06\u5f53\u7ec4\u88c5\u5b8c\u6210\u540e\u53ef\u4ee5\u8fdb\u884c\u90a3\u4e9b\u4e0b\u6e38\u5206\u6790\u6765\u6316\u6398\u6211\u4eec\u5173\u6ce8\u7684\u751f\u7269\u5b66\u95ee\u9898\u3002<br \/><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;text-align: left;letter-spacing: 0.034em;font-size: 14px;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491051&idx=1&sn=ffd92607626bf616ce250341225744d1&chksm=cf7c8d2ef80b043823d1034a72af50c0c6341dda5e226e084e935f8a486b4d35116893865cd5&scene=21#wechat_redirect\" textvalue=\"\u5c0f\u679c\u4e09\u5206\u949f\u6559\u4f1a\u4f60\u5982\u4f55\u4f7f\u7528Trinity\u505a\u8f6c\u5f55\u672c\u7ec4\u88c5\uff08\u4e0a\uff09\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">\u5c0f\u679c\u4e09\u5206\u949f\u6559\u4f1a\u4f60\u5982\u4f55\u4f7f\u7528Trinity\u505a\u8f6c\u5f55\u672c\u7ec4\u88c5\uff08\u4e0a\uff09<\/a><br \/><\/span><\/p>\n<\/section>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u770b\u5427<\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 20px;\"><em><strong><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">1.\u8f6c\u5f55\u672c\u4e30\u5ea6<\/span><\/strong><\/em><\/span><strong><span style=\"font-family: \u7b49\u7ebf;font-size: 12pt;background: rgb(255, 255, 0);\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p style=\"text-align: center;\"><span style=\"mso-spacerun:"yes";font-family:\u5b8b\u4f53;mso-ascii-font-family:Calibri;mso-hansi-font-family:Calibri;mso-bidi-font-family:"Times New Roman";font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5728\u8fdb\u884c\u5176\u5b83\u5206\u6790\u4e4b\u524d\uff0c\u6211\u4eec\u901a\u5e38\u5b66\u5bf9\u8f6c\u5f55\u672c\u548c\u57fa\u56e0\u7684\u4e30\u5ea6\u8fdb\u884c\u5b9a\u91cf\u3002\u5728Trinity\u4e2d\u63d0\u4f9b\u4e86\u8c03\u7528\u4e09\u79cd\u4e0d\u540c\u8f6f\u4ef6\u7684\u811a\u672c\uff0cRSEM\uff0ckallisto\u548csalmon\u3002\u503c\u5f97\u6ce8\u610f\u7684\u662fTrinity\u5e76\u6ca1\u6709\u540c\u65f6\u6253\u5305\u5b89\u88c5\u597d\u8fd9\u4e09\u4e2a\u8f6f\u4ef6\uff0c\u9700\u8981\u6211\u4eec\u81ea\u5df1\u4e0b\u8f7d\u5e76\u914d\u7f6e\u597d\u76f8\u5bf9\u5e94\u7684\u73af\u5883\u53d8\u91cf\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u4f7f\u7528\u4e00\u4e0b\u9762\u7684\u811a\u672cperl\u811a\u672c\u8fdb\u884c\u8ba1\u7b97<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<h2 style=\"text-align: center;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><o:p><\/o:p><\/span><\/h2>\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=\"shell\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/util\/align_and_estimate_abundance.pl<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e3b\u8981\u53c2\u6570\u5982\u4e0b\uff1a<\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code><span class=\"code-snippet_outer\"># --transcripts <string>: \u8f6c\u5f55\u672c\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"># --seqType <string>: fq|fa<\/span><\/code><code><span class=\"code-snippet_outer\"># \u82e5\u4e3apaired-end\u6570\u636e\uff1a--left <string>: \u5de6\u7aefreads\u6587\u4ef6 --right <string>: \u53f3\u7aefreads\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"># single-end\u6570\u636e\uff1a--single <string>: \u539f\u59cbreads\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"># --est_method <string>: RSEM|kallisto|salmon<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u6bd4\u5982\u8bf4\u6211\u4eecRSEM\u6765\u8fdb\u884c\u5b9a\u91cf\uff0c\u76f8\u5173\u547d\u4ee4\u5982\u4e0b\uff1a<o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\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=\"swift\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/util\/align_and_estimate_abundance.pl --transcript Trinity.fasta --est_method RSEM --aln_method bowtie --seqType fq --left reads_1.fq --right reads_2.fq --trinity_mode --prep_reference --output_dir rsem_outdir<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e4b\u540e\u4f1a\u8fd4\u8fd8\u4e24\u4e2a\u8f93\u51fa\u6587\u4ef6\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><br \/><\/span><\/p>\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=\"css\"><code><span class=\"code-snippet_outer\">\u2019RSEM.isoforms.results\u2019\u3001\u2019RSEM.genes.results\u2019<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u57fa\u56e0\u5206\u578b\u7684\u7ed3\u679c\u5982\u4e0b\u6240\u793a\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.32416787264833574\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_tDAzLUAhLdibIVrEEzqdK6XTvwgicg-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecdL2vlkV15jZeBgYRQKK1ZWsl72mtDAzLUAhLdibIVrEEzqdK6XTvwgicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"691\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e86\u4e00\u4e2a\u8f6c\u5f55\u672c\uff0c\u8bb0\u5f55\u4e86\u8f6c\u5f55\u672c\u7684\u957f\u5ea6\uff0c\u6709\u6548\u957f\u5ea6\uff0c\u671f\u671b\u6570\u91cf\uff0cTPM\u548cFPKM\uff0c\u53ef\u4ee5\u770b\u5230\u7b2c\u4e8c\u884c\u8fd9\u4e2a\u57fa\u56e0\u6709\u7740\u6700\u9ad8\u7684\u8868\u8fbe\u91cf\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u81f3\u6b64\uff0c\u6211\u4eec\u53ef\u4ee5\u5bf9\u6bcf\u4e2a\u6837\u672c\u6784\u5efa\u8f6c\u5f55\u672c\u548c\u57fa\u56e0\u7684\u8868\u8fbe\u77e9\u9635\uff0c\u4f7f\u7528\u4e0b\u9762\u8fd9\u4e2a\u811a\u672c\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><br \/><\/p>\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=\"objectivec\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/util\/abundance_estimates_to_matrix.pl<\/span><\/code><code><span class=\"code-snippet_outer\"># --est_method <string>: RSEM|kallisto|salmon<\/span><\/code><code><span class=\"code-snippet_outer\"># --gene_trans_map <string>: \u57fa\u56e0\u548c\u8f6c\u5f55\u672c\u7684\u8f6c\u6362\u6587\u4ef6<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4f8b\u5b50\u5982\u4e0b\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\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=\"shell\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/util\/abundance_estimates_to_matrix.pl --est_method RSEM --gene_trans_map Trinity.fasta.gene_trans_map --name_sample_by_basedir<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u4f1a\u5f97\u5230\u4ee5\u4e0b\u4e09\u4e2a\u6587\u4ef6\uff1a<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018RSEM.isoform.count.matrix\u2019: \u539f\u59cbcounts\u6570\u636e<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018RSEM.isoform.TPM.not_cross_norm\u2019: TPM\u8868\u8fbe\u91cf\uff08\u6ca1\u6709\u8fdb\u884c\u8de8\u6837\u672c\u5f52\u4e00\u5316\uff09<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018RSEM.isoform.TMM.EXPR.matrix\u2019: TMM\u5f52\u4e00\u5316\u7684\u8868\u8fbe\u503c<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 20px;\"><em><strong>2.\u5dee\u5f02\u8868\u8fbe\u5206\u6790<\/strong><\/em><\/span><strong><span style=\"font-family: \u7b49\u7ebf;font-size: 12pt;background: rgb(255, 255, 0);\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"font-size: 14px;font-family: Optima-Regular, PingFangTC-light;\">\u5f97\u5230\u4e86\u8868\u8fbe\u77e9\u9635\u4e4b\u540e\u6211\u4eec\u5c31\u53ef\u4ee5\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u4e86\uff0cTrinity\u4e2d\u4f7f\u7528\u7684\u662fEdgeR\u8fd9\u4e2aR\u5305\u6765\u505a\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u540c\u6837\u9700\u8981\u54b1\u4eec\u7684\u7cfb\u7edf\u4e2d\u88c5\u6709\u76f8\u5bf9\u5e94\u7684R\u73af\u5883\u548c\u8f6f\u4ef6\u5305\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: Optima-Regular, PingFangTC-light;\">\u5177\u4f53\u811a\u672c\u547d\u4ee4\u548c\u53c2\u6570\u5982\u4e0b\u6240\u793a\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/Analysis\/DifferentialExpression\/run_DE_analysis.pl<\/span><\/code><code><span class=\"code-snippet_outer\"># --matrix|m <string>: \u539f\u59cbcount\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\"># --method <string>: edgeR|DESeq2|voom<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u8fd0\u884c\u4ee5\u4e0b\u811a\u672c\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\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=\"shell\"><code><span class=\"code-snippet_outer\">$ TRINITY_HOME\/Analysis\/DifferentialExpression\/run_DE_analysis.pl --matrix RSEM.isoform.count.matrix --method edgeR \u2013samples_file samples_described.txt<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5173\u4e8eedgeR\u7684\u53c2\u6570\u8bbe\u7f6e\u53ef\u4ee5\u67e5\u8be2<\/span><span style=\"color: rgb(5, 99, 193);text-decoration: underline;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">edgeR manual<\/span><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u7136\u540e\u6211\u4eec\u4f1a\u5f97\u5230\u4e09\u4e2a\u6587\u4ef6\uff0c\u5206\u522b\u662f\uff1a<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018${prefix}.sampleA_vs_sampleB.${method}.DE_results\u2019<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u2018${prefix}.sampleA_vs_sampleB.${method}.MA_n_Volcano.pdf\u2019<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">${prefix}.sampleA_vs_sampleB.${method}.Rscript\u2019<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770bDE_results\u6587\u4ef6\u7684\u5934\u51e0\u884c\uff0c\u8bb0\u5f55\u7740log fold change\u548c\u76f8\u5bf9\u5e94\u7684\u7edf\u8ba1\u91cf\uff08Pvalue\uff0cFDR\u77eb\u6b63\uff09<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7734487734487735\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ric7Roia2TLQ9m7HMffibgXs1v8LDA-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecd1S1CKbs51fjXCSYvUVjPAialaKeWric7Roia2TLQ9m7HMffibgXs1v8LDA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u540c\u65f6\u8fd8\u6709\u706b\u5c71\u56fe<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.46320346320346323\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_TgtOC9s2G7EaUJ2Eicug4YjnkasicA-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecdFiauVu7OST9alKm1E752jdurbkZTgtOC9s2G7EaUJ2Eicug4YjnkasicA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u5bf9\u4e8e\u5dee\u5f02<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u8868\u8fbe<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><span style=\"font-family:\u7b49\u7ebf;\">\u7684\u4e00\u4e2a\u6bd4\u8f83\u521d\u59cb\u7684\u5206\u6790\u5c31\u662f\u53bb\u83b7\u53d6\u90a3\u4e9b\u524d\u540e\u8868\u8fbe\u5dee\u5f02\u6781\u5927\u7684\u8f6c\u5f55\u672c\uff08\u6700\u663e\u8457\u7684<\/span><span style=\"font-family:\u7b49\u7ebf;\">FDR\u548cfold<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">–<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">change\uff09\uff0c<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\">\u7136\u540e\u6839\u636e\u4e0d\u540c\u7684\u8868\u8fbe\u6a21\u5f0f\u5c06\u8fd9\u4e9b\u8f6c\u5f55\u672c\u5212\u5206\u805a\u7c7b\u3002\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u811a\u672c\u8fdb\u884c\u805a\u7c7b<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/Analysis\/DifferentialExpression\/analyze_diff_expr.pl <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> --matrix <string>: TMM.EXPR.matrix<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> -P <<span class=\"code-snippet__built_in\">float<\/span>>: pvalue\u9608\u503c<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> -C <<span class=\"code-snippet__built_in\">float<\/span>>: \u6700\u5c0f\u7684fold change\u6570<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5982\u5c0f\u679c\u4e0b\u9762\u4e3e\u7684\u4f8b\u5b50\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/Analysis\/DifferentialExpression\/analyze_diff_expr.pl --matrix ..\/Trinity_trans.TMM .EXPR.matrix -P 1e-3 -C 2<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;\"><span style=\"font-size: 14px;font-family: \u7b49\u7ebf;\">\u7136\u540e\u6211\u4eec\u5c31\u80fd\u5f97\u5230\u5982\u4e0b\u5dee\u5f02\u57fa\u56e0\u548c\u4e0d\u540c\u6837\u672c\u7684\u70ed\u56fe\uff1a<\/span><span style=\"font-family: \u7b49\u7ebf;font-size: 12pt;\"><o:p><\/o:p><\/span><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1.092485549132948\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_tqjcst3WBZq7fWGiboR6REqicZxS9A-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecdxmh22XEKN8EjGaEbgqSXqIaDestqjcst3WBZq7fWGiboR6REqicZxS9A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 20px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><em><strong><span style=\"font-size: 20px;font-weight: bold;\"><br \/><\/span><\/strong><\/em><\/span><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 20px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><em><strong><span style=\"font-size: 20px;font-weight: bold;\">3.<\/span><span style=\"font-size: 20px;\">\u8f6c\u5f55\u672c\u529f\u80fd\u6ce8\u91ca<\/span><\/strong><\/em><\/span><strong><span style=\"font-family: \u7b49\u7ebf;font-size: 12pt;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p><span style=\"font-size: 14px;\"><span style=\"font-size: 14px;font-family: \u7b49\u7ebf;\"><\/span><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5728\u6211\u4eec\u5f97\u5230\u4e86\u62fc\u63a5\u7684\u8f6c\u5f55\u672c\u4ee5\u53ca\u76f8\u5e94\u7684\u57fa\u56e0\u96c6\u4e4b\u540e\uff0c\u6211\u4eec\u81ea\u7136\u800c\u7136\u60f3\u77e5\u9053\u8fd9\u4e9b\u57fa\u56e0\u5bcc\u96c6\u5728\u4ec0\u4e48\u6837\u7684\u529f\u80fd\u4e0a\u3002\u540c\u6837\u7684\uff0c\u54b1\u4eec\u5f3a\u5927\u7684Trinity\u63d0\u4f9b\u4e86\u4e00\u5957\u5b8c\u6574\u7684\u6d41\u7a0b\u3002\u9996\u5148\u6211\u4eec\u901a\u8fc7\u4ee5\u4e0b\u811a\u672c\u6765\u83b7\u53d6\u6bcf\u4e2a\u57fa\u56e0\u6240\u5bf9\u5e94\u7684GO term\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\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=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/util\/extract_GO_assignments_from_Trinotate_xls.pl --Trinoate_xls trinotate.xls -G --include_ancestral_terms > go_annotations.txt<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u7136\u540e\u6211\u4eec\u518d\u4f7f\u7528Bioconductor\u4e2d\u7684\u5305GOseq\u8fdb\u884c\u529f\u80fd\u5bcc\u96c6\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/Analysis\/DifferentialExpression\/run_GOseq.pl --factor_labeling factor_labeling.txt --GO_assignments go_annotations.txt --lengths gene.lengths.txt<\/span><\/code><\/pre>\n<\/section>\n<p style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;text-align: left;text-wrap: wrap;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5176\u4e2d\u2019factor_labeling.txt\u2019\u8fd9\u4e2a\u6587\u4ef6\u8bb0\u8f7d\u7740\u4e0d\u540c\u6837\u672c\u95f4\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u96c6\uff0c\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:12.0000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.170767004341534\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_aH8yqPaLHqNEaVUFGUeTHxyFWYicQA-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecdNC0l3I5htlN7EKNbDykeGx8ibLiaH8yqPaLHqNEaVUFGUeTHxyFWYicQA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"691\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u800c\u5bf9\u4e8e\u2018gene.lengths.txt\u2019\u8fd9\u4e2a\u6587\u4ef6\uff0c\u6211\u4eec\u4f7f\u7528\u5982\u4e0b\u547d\u4ee4\u8fdb\u884c\u521b\u5efa\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;text-align: left;text-wrap: wrap;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/util\/misc\/fasta_seq_length.pl Trinity.fasta > Trinity.fasta.seq_lengths<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">$<\/span> TRINITY_HOME\/util\/misc\/TPM_weighted_gene_length.py --gene_trans_map trinity_out_dir\/Trinity.fasta.gene_trans_map --trans_lengths Trinity.fasta.seq_lens --TPM_matrix isoforms.TMM.EXPR.matrix > Trinity.gene_lengths.txt<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5728\u6700\u540e\u6211\u4eec\u5c31\u4f1a\u5f97\u5230\u4e00\u4e2a\u5982\u4e0b\u7684\u56fe\u6807\uff0c\u5176\u4e2d\u8bb0\u5f55\u7740\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u5bcc\u96c6\u5230\u7684\u529f\u80fd\u901a\u8def\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:Consolas;mso-fareast-font-family:\u7b49\u7ebf;mso-bidi-font-family:'Times New Roman';color:rgb(51,51,51);font-size:10.5000pt;mso-font-kerning:1.0000pt;background:rgb(238,239,240);mso-shading:rgb(238,239,240);\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.15050651230101303\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_mUKEvcLoBgokUicmEO4TfubUzsdUbw-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyBMiaebYV0wRXKtNfxorecd5LkZ9LUU4Jl1aj2NBDBAiba2stmUKEvcLoBgokUicmEO4TfubUzsdUbw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"691\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4ee5\u4e0a\u5c31\u662f\u4f7f\u7528Trinity\u8fdb\u884cde novo\u8f6c\u5f55\u672c\u62fc\u63a5\u3001\u4e0b\u6e38\u5206\u6790\u7684\u5168\u90e8\u5185\u5bb9\uff0c\u5982\u679c\u4f60\u6709\u4ec0\u4e48\u95ee\u9898\u7684\u8bdd\u6b22\u8fce\u548c\u5c0f\u679c\u8ba8\u8bba\uff01<\/span><span style=\"text-align: center;letter-spacing: 0.034em;\"><\/span><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, 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