{"id":24861,"date":"2024-01-17T10:46:37","date_gmt":"2024-01-17T02:46:37","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24861"},"modified":"2024-01-17T10:46:40","modified_gmt":"2024-01-17T02:46:40","slug":"%e5%b0%8f%e6%9e%9c%e4%b8%89%e5%88%86%e9%92%9f%e6%95%99%e4%bc%9a%e4%bd%a0%e5%a6%82%e4%bd%95%e5%af%b9trinity%e8%bd%ac%e5%bd%95%e6%9c%ac%e8%bf%9b%e8%a1%8c%e4%b8%8b%e6%b8%b8%e5%88%86%e6%9e%90%ef%bc%88","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24861","title":{"rendered":"\u5c0f\u679c\u4e09\u5206\u949f\u6559\u4f1a\u4f60\u5982\u4f55\u5bf9Trinity\u8f6c\u5f55\u672c\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\uff08\u4e0b\uff09"},"content":{"rendered":"

\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<\/p>\n

\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u770b\u5427<\/p>\n

    \n
  1. \u8f6c\u5f55\u672c\u4e30\u5ea6<\/strong><\/li>\n<\/ol>\n

    \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<\/p>\n

    \u6211\u4eec\u4f7f\u7528\u4e00\u4e0b\u9762\u7684\u811a\u672cperl\u811a\u672c\u8fdb\u884c\u8ba1\u7b97<\/p>\n

    $ TRINITY_HOME\/util\/align_and_estimate_abundance.pl<\/p>\n

    \u4e3b\u8981\u53c2\u6570\u5982\u4e0b\uff1a<\/p>\n

    # –transcripts <string>: \u8f6c\u5f55\u672c\u6587\u4ef6<\/p>\n

    # –seqType <string>: fq|fa<\/p>\n

    # \u82e5\u4e3apaired-end\u6570\u636e\uff1a –left <string>: \u5de6\u7aefreads\u6587\u4ef6 –right <string>: \u53f3\u7aefreads\u6587\u4ef6<\/p>\n

    # single-end\u6570\u636e\uff1a–single <string>: \u539f\u59cbreads\u6587\u4ef6<\/p>\n

    # –est_method <string>: RSEM|kallisto|salmon<\/p>\n

    \u6bd4\u5982\u8bf4\u6211\u4eecRSEM\u6765\u8fdb\u884c\u5b9a\u91cf\uff0c\u76f8\u5173\u547d\u4ee4\u5982\u4e0b\uff1a<\/p>\n

    $ 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<\/p>\n

    \u4e4b\u540e\u4f1a\u8fd4\u8fd8\u4e24\u4e2a\u8f93\u51fa\u6587\u4ef6\uff1a<\/p>\n

    \u2019RSEM.isoforms.results\u2019\u3001\u2019RSEM.genes.results\u2019<\/p>\n

    \u57fa\u56e0\u5206\u578b\u7684\u7ed3\u679c\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n

    <\/p>\n

    \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<\/p>\n

    \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<\/p>\n

    $ TRINITY_HOME\/util\/abundance_estimates_to_matrix.pl<\/p>\n

    # –est_method <string>: RSEM|kallisto|salmon<\/p>\n

    # –gene_trans_map <string>: \u57fa\u56e0\u548c\u8f6c\u5f55\u672c\u7684\u8f6c\u6362\u6587\u4ef6<\/p>\n

    \u4f8b\u5b50\u5982\u4e0b\uff1a<\/p>\n

    $ TRINITY_HOME\/util\/abundance_estimates_to_matrix.pl –est_method RSEM –gene_trans_map Trinity.fasta.gene_trans_map –name_sample_by_basedir<\/p>\n

    \u6211\u4eec\u4f1a\u5f97\u5230\u4ee5\u4e0b\u4e09\u4e2a\u6587\u4ef6\uff1a<\/p>\n

    \u2018RSEM.isoform.count.matrix\u2019: \u539f\u59cbcounts\u6570\u636e<\/p>\n

    \u2018RSEM.isoform.TPM.not_cross_norm\u2019: TPM\u8868\u8fbe\u91cf\uff08\u6ca1\u6709\u8fdb\u884c\u8de8\u6837\u672c\u5f52\u4e00\u5316\uff09<\/p>\n

    \u2018RSEM.isoform.TMM.EXPR.matrix\u2019: TMM\u5f52\u4e00\u5316\u7684\u8868\u8fbe\u503c<\/p>\n

      \n
    1. \u5dee\u5f02\u8868\u8fbe\u5206\u6790<\/strong><\/li>\n<\/ol>\n

      \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<\/p>\n

      \u5177\u4f53\u811a\u672c\u547d\u4ee4\u548c\u53c2\u6570\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n

      $ TRINITY_HOME\/Analysis\/DifferentialExpression\/run_DE_analysis.pl<\/p>\n

      # –matrix|m <string>: \u539f\u59cbcount\u77e9\u9635<\/p>\n

      # –method <string>: edgeR|DESeq2|voom<\/p>\n

      \u8fd0\u884c\u4ee5\u4e0b\u811a\u672c\uff1a<\/p>\n

      $ TRINITY_HOME\/Analysis\/DifferentialExpression\/run_DE_analysis.pl –matrix RSEM.isoform.count.matrix –method edgeR \u2013samples_file samples_described.txt<\/p>\n

      \u5173\u4e8eedgeR\u7684\u53c2\u6570\u8bbe\u7f6e\u53ef\u4ee5\u67e5\u8be2edgeR manual<\/a>\u3002<\/p>\n

      \u7136\u540e\u6211\u4eec\u4f1a\u5f97\u5230\u4e09\u4e2a\u6587\u4ef6\uff0c\u5206\u522b\u662f\uff1a<\/p>\n

      \u2018${prefix}.sampleA_vs_sampleB.${method}.DE_results\u2019<\/p>\n

      \u2018${prefix}.sampleA_vs_sampleB.${method}.MA_n_Volcano.pdf\u2019<\/p>\n

      ${prefix}.sampleA_vs_sampleB.${method}.Rscript\u2019<\/p>\n

      \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<\/p>\n

      <\/p>\n

      \u540c\u65f6\u8fd8\u6709\u706b\u5c71\u56fe<\/p>\n

      <\/p>\n

      \u5bf9\u4e8e\u5dee\u5f02\u8868\u8fbe\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\u7684FDR\u548cfold-change\uff09\uff0c\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<\/p>\n

      $ TRINITY_HOME\/Analysis\/DifferentialExpression\/analyze_diff_expr.pl<\/p>\n

      # –matrix <string>: TMM.EXPR.matrix<\/p>\n

      # -P <float>: pvalue\u9608\u503c<\/p>\n

      # -C <float>: \u6700\u5c0f\u7684fold change\u6570<\/p>\n

      \u5982\u5c0f\u679c\u4e0b\u9762\u4e3e\u7684\u4f8b\u5b50\uff1a<\/p>\n

      $ TRINITY_HOME\/Analysis\/DifferentialExpression\/analyze_diff_expr.pl –matrix ..\/Trinity_trans.TMM .EXPR.matrix -P 1e-3 -C 2<\/p>\n

      \u7136\u540e\u6211\u4eec\u5c31\u80fd\u5f97\u5230\u5982\u4e0b\u5dee\u5f02\u57fa\u56e0\u548c\u4e0d\u540c\u6837\u672c\u7684\u70ed\u56fe\uff1a<\/p>\n

      <\/p>\n

        \n
      1. \u8f6c\u5f55\u672c\u529f\u80fd\u6ce8\u91ca<\/strong><\/li>\n<\/ol>\n

        \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<\/p>\n

        $ TRINITY_HOME\/util\/extract_GO_assignments_from_Trinotate_xls.pl –Trinoate_xls trinotate.xls -G –include_ancestral_terms > go_annotations.txt<\/p>\n

        \u7136\u540e\u6211\u4eec\u518d\u4f7f\u7528Bioconductor\u4e2d\u7684\u5305GOseq\u8fdb\u884c\u529f\u80fd\u5bcc\u96c6\uff1a<\/p>\n

        $ TRINITY_HOME\/Analysis\/DifferentialExpression\/run_GOseq.pl –factor_labeling factor_labeling.txt –GO_assignments go_annotations.txt –lengths gene.lengths.txt<\/p>\n

        \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<\/p>\n

        <\/p>\n

        \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<\/p>\n

        $ TRINITY_HOME\/util\/misc\/fasta_seq_length.pl Trinity.fasta > Trinity.fasta.seq_lengths<\/p>\n

        $ 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<\/p>\n

        \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<\/p>\n

        <\/p>\n

        \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\u5662\ud83d\ude0a\ud83d\ude0a<\/p>\n

        \u66f4\u591a\u751f\u4fe1\u5c0f\u5de5\u5177\u53ef\u67e5\u8be2\u4e91\u5e73\u53f0\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/p>\n","protected":false},"excerpt":{"rendered":"

        \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 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24861"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=24861"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24861\/revisions"}],"predecessor-version":[{"id":24873,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24861\/revisions\/24873"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24861"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24861"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24861"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}