{"id":1334,"date":"2024-12-03T20:01:03","date_gmt":"2024-12-03T12:01:03","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1334"},"modified":"2025-11-19T18:31:00","modified_gmt":"2025-11-19T10:31:00","slug":"cafe-5%ef%bc%9a%e5%9f%ba%e5%9b%a0%e5%ae%b6%e6%97%8f%e7%9a%84%e6%89%a9%e5%bc%a0%e4%b8%8e%e6%94%b6%e7%bc%a9","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2024\/12\/03\/cafe-5%ef%bc%9a%e5%9f%ba%e5%9b%a0%e5%ae%b6%e6%97%8f%e7%9a%84%e6%89%a9%e5%bc%a0%e4%b8%8e%e6%94%b6%e7%bc%a9\/","title":{"rendered":"CAFE 5\uff1a\u57fa\u56e0\u5bb6\u65cf\u7684\u6269\u5f20\u4e0e\u6536\u7f29"},"content":{"rendered":"\t\t
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CAFE 5\uff1a\u57fa\u56e0\u5bb6\u65cf\u7684\u6269\u5f20\u4e0e\u6536\u7f29<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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1. \u8f6f\u4ef6\u4e0b\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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### \u521b\u5efa\u5206\u6790\u73af\u5883<\/p>

mamba create -n Gene_family_expend_shrink<\/p>

### \u4e0b\u8f7d cafe\u00a0<\/p>

mamba install bioconda::cafe<\/p>

### \u4e0b\u8f7d orthofinder<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2 \u57fa\u56e0\u5bb6\u65cf\u805a\u7c7b<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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### \u8fd0\u884corthofinder\u8fdb\u884c\u57fa\u56e0\u5bb6\u65cf\u7684\u805a\u7c7b<\/p>

orthofinder -f .\/quanbu -o Orthofinder_result_20241128_pep_quanbu -a 30 -t 30<\/p>

# -f \u8f93\u5165\u6587\u4ef6\u5939\uff08\u5305\u542b\u6240\u6709\u5f85\u5206\u6790\u7269\u79cd\u7684\u86cb\u767d\u5e8f\u5217\u7684\u6587\u4ef6\u5939\uff09<\/p>

# -o \u8f93\u51fa\u7ed3\u679c\u6587\u4ef6\u5939\u7684\u540d\u79f0<\/p>

# -a Parallel sequence search \u8fd0\u884c\u7684\u7ebf\u7a0b\u6570<\/p>

# -t Paralle analysis \u8fd0\u884c\u7684\u7684\u7ebf\u7a0b\u6570<\/p>

### \u8f93\u51fa\u7ed3\u679c<\/p>

Orthogroups\/Orthogroups.GeneCount.tsv \uff1a<\/strong>\u540e\u7eed\u5206\u6790\u7684\u4e3b\u8981\u7ed3\u679c<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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3 \u57fa\u56e0\u5bb6\u65cf\u7684\u6269\u5f20\u4e0e\u6536\u7f29\u5206\u6790<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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CAFE \u7684\u8f93\u5165\u6587\u4ef6\u6709\u4e24\u4e2a\uff0c\uff081\uff09\u7b26\u5408\u4e8c\u5206\u53c9\u7684\u8d85\u5ea6\u91cf\u6811\uff08\u5e26\u6709\u5206\u6b67\u65f6\u95f4\u7684\u7cfb\u7edf\u53d1\u80b2\u6811\uff09\uff0c\uff082\uff09\u7269\u79cd\u548c\u57fa\u56e0\u5bb6\u65cf\u6570\u91cf\u7684\u5bf9\u5e94\u8868\u3002\u5176\u4e2d\uff081\uff09\u5e94\u8be5\u662f\u4f30\u7b97\u5206\u6b67\u65f6\u95f4\u540e\u751f\u6210\u7684\u7ed3\u679c\uff0c\uff082\uff09\u53ef\u4ee5\u901a\u8fc7Orthogroups\/Orthogroups.GeneCount.tsv\u8fdb\u884c\u683c\u5f0f\u8f6c\u6362\u751f\u6210\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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# Orthogroups.GeneCount.tsv\u8f6c\u6362\u751f\u6210Gene_family.txt<\/p>\n

awk -v OFS=\"\\t\" '{$NF=null;print $1,$0}' Orthogroups.GeneCount.tsv |sed -E -e 's\/Orthogroup\/desc\/' -e 's\/_[^\\t]+\/\/g' > gene_families.txt<\/p>\n

# \u5bf9\u57fa\u56e0\u5bb6\u65cf\u8fdb\u884c\u8fc7\u6ee4\uff08\u53ef\u9009\u6b65\u9aa4\uff09<\/p>\n

awk 'NR==1 || $3<100 && $4<100 && $5<100 && $6<100 && $7<100 && $8<100 && $9<100 && $10<100 && $11<100 && $12<100 && $13<100 && $14<100 && $15<100 && $16<100 && $17<100 {print $0}' gene_families.txt > gene_families_filter.txt<\/p>\n

# \u8fd0\u884cCAFE<\/p>\n

cafe5 --infile gene_families.txt --tree Reroot_Complete_Time_point_tree.tre --cores 100 --output_prefix cafe_out<\/p>\n

# --infile \u7269\u79cd\u548c\u57fa\u56e0\u5bb6\u65cf\u6570\u91cf\u7684\u5bf9\u5e94\u8868\uff081\uff09<\/p>\n

# --tree \u8d85\u5ea6\u91cf\u6811\uff082\uff09<\/p>\n

# --cores \u8fd0\u884c\u7684\u7ebf\u7a0b\u6570<\/p>\n

# --output_prefix \u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00<\/p><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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4 \u8f93\u51fa\u7ed3\u679c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# XXX_asr.tre<\/p>

# XXX_branch_probabilities.tab<\/p>

# XXX_change.tab<\/p>

# XXX_clade_results.txt \u6700\u91cd\u8981\u7684\u7ed3\u679c\uff0c\u663e\u793a\u4e86\u8fdb\u5316\u6811\u8282\u70b9\u4e2d\u6269\u5f20\u548c\u6536\u7f29\u7684\u57fa\u56e0<\/strong><\/p>

# XXX_count.tab<\/p>

# XXX_family_likelihoods.txt<\/p>

# XXX_family_results.txt<\/p>

# XXX_report.cafe<\/p>

# XXX_results.txt<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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5. \u63d0\u53d6\u6536\u7f29\u548c\u6269\u5f20\u7684\u57fa\u56e0\u8fdb\u884c\u5bcc\u96c6\u5206\u6790<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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5.1 \u63d0\u53d6\u6269\u5f20\u548c\u6536\u7f29\u7684\u57fa\u56e0\u57fa\u56e0<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\n\t\t\t\t\n\t\t\t\t\tcat Gamma_change.tab |cut -f1,15|grep \"+[1-9]\" >sample.expanded #\u63d0\u53d6Gamma_change.tab\u7b2c15\u5217\u4ee3\u8868\u7269\u79cdsample\u7684\u6269\u5f20\u7684orthogroupsID\ncat Gamma_change.tab |cut -f1,15|grep \"-\" >sample.contracted  #\u63d0\u53d6Gamma_change.tab\u7b2c15\u5217\u4ee3\u8868\u7269\u79cdsample\u7684\u6536\u7f29\u7684orthogroupsID\ngrep \"sample<13>\\*\" Gamma_asr.tre > sample_significant_trees.tre # \u6839\u636esample ID\u548c\u7f16\u53f7\u63d0\u53d6sample\u5206\u652f\u7684\u57fa\u56e0\u5bb6\u65cf\u663e\u8457\u6269\u5f20\u6216\u6536\u7f29\u7684\u57fa\u56e0\u5bb6\u65cf\u6811\uff08Gamma_asr.tre\u6587\u4ef6\u4e2d\u9ed8\u8ba4\u4ee5p<0.05\u4e3a\u6807\u51c6\u5224\u65ad\u53d8\u5316\u662f\u5426\u663e\u8457\uff09\ngrep -E -o \"OG[0-9]+\" sample_significant_trees.tre > sample_significant.ogs # \u63d0\u53d6sample\u5206\u652f\u663e\u8457\u53d8\u5316\u7684OG IDs \uff08\u9ed8\u8ba4\u4ee5p<0.05\u4e3a\u6807\u51c6\uff09\nawk '$2 <0.01 {print $1}' Gamma_family_results.txt >p0.01_significant.ogs # \u4ee5p<0.01\u4e3a\u6807\u51c6\u63d0\u53d6\u6240\u6709\u663e\u8457\u6269\u5f20\u6216\u6536\u7f29\u7684orthogroupsID\uff08\u6839\u636e\u60c5\u51b5\u8c03\u6574\uff0c\u5e38\u7528p<0.05\u6216p<0.01\uff09\ngrep -f sample_significant.ogs p0.01_significant.ogs > sample_p0.01_significant.ogs # \u63d0\u53d6\u4ee5p<0.01\u4e3a\u6807\u51c6\u5224\u65ad\u663e\u8457\u6027\u7684sample\u5206\u652f\u57fa\u56e0\u5bb6\u65cf\u663e\u8457\u53d8\u5316\u7684OG IDs\u3002\ngrep -f sample_p0.01_significant.ogs sample.expanded |cut -f1 >s ample.expanded.significant #\u63d0\u53d6\u663e\u8457\u6269\u5f20\u7684sample\u7269\u79cd\u7684orthogroupsID\ngrep -f sample_p0.01_significant.ogs sample.contracted |cut -f1 > sample.contracted.significant #\u63d0\u53d6\u663e\u8457\u6536\u7f29\u7684sample\u7269\u79cd\u7684orthogroupsID\ngrep -f sample.expanded.significant .\/OrthoFinder\/Results_Oct14\/Orthogroups\/Orthogroups.txt |sed \"s\/ \/\\n\/g\"|grep \"bv\" |sort -k 1.3n |uniq >sample.expanded.significant.genes #\u63d0\u53d6\u663e\u8457\u6269\u5f20\u7684\u57fa\u56e0\u5217\u8868\uff0c\u5047\u8bbe\u57fa\u56e0ID\u662fbv\u7684\u524d\u7f00\u3002\ngrep -f sample.contracted.significant .\/OrthoFinder\/Results_Oct14\/Orthogroups\/Orthogroups.txt sed \"s\/ \/\\n\/g\"|grep \"bv\" |sort -k 1.3n |uniq >sample.contracted.significant.genes #\u63d0\u53d6\u663e\u8457\u6536\u7f29\u7684\u57fa\u56e0\u5217\u8868\uff0c\u5047\u8bbe\u57fa\u56e0ID\u662fbv\u7684\u524d\u7f00\u3002\nseqkit grep -f sample.expanded.significant.genes sample.pep.fa >sample.expanded.significant.pep.fa #\u63d0\u53d6\u663e\u8457\u6269\u5f20\u7684\u57fa\u56e0\u5e8f\u5217\nseqkit grep -f sample.contracted.significant.genes sample.pep.fa >sample.contracted.significant.pep.fa #\u63d0\u53d6\u663e\u8457\u6536\u7f29\u7684\u57fa\u56e0\u5e8f\u5217<\/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-61f4a6a elementor-widget elementor-widget-heading\" data-id=\"61f4a6a\" 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<h3 class=\"elementor-heading-title elementor-size-default\">5.2 \u5bcc\u96c6\u5206\u6790<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ce3c1e6 elementor-widget elementor-widget-text-editor\" data-id=\"ce3c1e6\" 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>\u5bcc\u96c6\u5206\u6790\u8981\u51c6\u5907GO\u548cKEGG\u6ce8\u91ca\u7684\u7ed3\u679c\u6587\u4ef6\uff0c\u6587\u4ef6\u7684\u683c\u5f0f\u4e3a\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0ID\uff0c\u7b2c\u4e8c\u5217\u4e3a\u57fa\u56e0ID\u5bf9\u5e94\u7684KO\u6216GO\u53f7\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-24bed2b elementor-widget elementor-widget-text-editor\" data-id=\"24bed2b\" 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># KEGG \u6ce8\u91ca\u7ed3\u679c\u6587\u4ef6\u683c\u5f0f<br \/>evm.TU.Chromosome_8_B.3367 K00001<br \/>evm.TU.Chromosome_4_B.3962 K00001<br \/>evm.TU.Chromosome_3_B.5527 K00001<br \/>evm.TU.Chromosome_8_B.3356 K00001<br \/>evm.TU.Chromosome_4_B.2409 K00001<br \/>evm.TU.Chromosome_8_B.3357 K00001<br \/>evm.TU.Chromosome_3_B.1839 K00001<br \/>evm.TU.Chromosome_4_B.2190 K00001<\/p><p># GO\u6ce8\u91ca\u7ed3\u679c\u6587\u4ef6\u683c\u5f0f<\/p><p>evm.model.Chromosome_3_B.1356 GO:0006979<br \/>evm.model.Chromosome_3_B.1367 GO:0010492<br \/>evm.model.Chromosome_4_B.331 GO:0006355<br \/>evm.model.Chromosome_9_B.2428 GO:0005634<br \/>evm.model.Chromosome_8_B.806 GO:0004497<br \/>evm.model.Chromosome_4_B.2710 GO:0003735<br \/>evm.model.Chromosome_5_B.3513 GO:0003729<\/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-fb6573a elementor-widget elementor-widget-text-editor\" data-id=\"fb6573a\" 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>GO\u548cKEGG\u7684\u5bcc\u96c6\u5206\u6790\u4f7f\u7528TBtools\u5b8c\u6210\uff0c\u6559\u7a0b\u53ef\u4ee5\u53c2\u8003TBtools\u7684\u5b98\u65b9\u6559\u7a0b<\/p><p>GO\u5bcc\u96c6\u6559\u7a0b\uff1a<a href=\"https:\/\/geekdaxue.co\/read\/cjchen@hirv8i\/wnve76\">https:\/\/geekdaxue.co\/read\/cjchen@hirv8i\/wnve76<\/a><\/p><p>KEGG\u5bcc\u96c6\u6559\u7a0b\uff1a<a href=\"https:\/\/geekdaxue.co\/read\/cjchen@hirv8i\/pohup4\">https:\/\/geekdaxue.co\/read\/cjchen@hirv8i\/pohup4<\/a><\/p><p>\u5bcc\u96c6\u5206\u6790\u9700\u8981\u7528\u5230\u7684\u6570\u636e\u5e93\u53ef\u4ee5\u901a\u8fc7TBtools\u8f6f\u4ef6\u4e0b\u8f7d\uff0c\u4f46\u662f\u53ef\u80fd\u4f1a\u56e0\u4e3a\u7f51\u7edc\u95ee\u9898\u4e0b\u8f7d\u5931\u8d25\uff0c\u6211\u628a\u5b83\u5b58\u5728\u4e86\u767e\u5ea6\u7f51\u76d8\u4e2d\uff0c\u9700\u8981\u8bf7\u81ea\u53d6\uff1a<a href=\"https:\/\/pan.baidu.com\/s\/1TvWrsp57FT9QT8H3Vf0gig\">https:\/\/pan.baidu.com\/s\/1TvWrsp57FT9QT8H3Vf0gig<\/a><\/p><p>\u00a0<\/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-272a718 elementor-widget elementor-widget-heading\" data-id=\"272a718\" 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<h3 class=\"elementor-heading-title elementor-size-default\">\u7ed8\u5236GO\u548cKEGG\u7684\u5bcc\u96c6\u56fe<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-0a1fbd0 elementor-widget elementor-widget-text-editor\" data-id=\"0a1fbd0\" 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>\u901a\u5e38KEGG\u548cGO\u4f1a\u53d6\u524d20\u4e2a\u6761\u76ee\uff08P value or Count or Enrichfator\uff09\u8fdb\u884c\u7ed8\u5236\uff0cGO\u7ed8\u5236\u4e3a\u5206\u7c7b\u67f1\u72b6\u56fe\uff0cKEGG\u7ed8\u5236\u4e3a\u6c14\u6ce1\u56fe\uff0c\u63a8\u8350\u4f7f\u7528Chiplot\u7f51\u7ad9\u8fdb\u884c\u7ed8\u56fe\uff0c\u5bf90\u57fa\u7840\u7684\u751f\u4fe1\u5c0f\u767d\u5f88\u53cb\u597d\u3002<\/p><p>\u6c14\u6ce1\u56fe\uff08KEGG\u5bcc\u96c6\uff09\u7ed8\u56fe\u7f51\u7ad9\uff1a<a href=\"https:\/\/www.chiplot.online\/enrich_plot.html\">https:\/\/www.chiplot.online\/enrich_plot.html<\/a><\/p><p>\u6c14\u6ce1\u56fe\uff08KEGG\u5bcc\u96c6\uff09\u7ed8\u56fe\u7f51\u7ad9\u4f7f\u7528\u6559\u7a0b\uff1a<a href=\"https:\/\/www.bilibili.com\/video\/BV1mP4y1w74C\/?vd_source=ac0301f422193d385c811b0bdbbd27ff\">https:\/\/www.bilibili.com\/video\/BV1mP4y1w74C\/?vd_source=ac0301f422193d385c811b0bdbbd27ff<\/a><\/p><p>\u5206\u7c7b\u67f1\u72b6\u56fe\uff08GO\u5bcc\u96c6\uff09\u7ed8\u56fe\u7f51\u7ad9\uff1a<a href=\"https:\/\/www.chiplot.online\/bar_plot_width_category.html\">https:\/\/www.chiplot.online\/bar_plot_width_category.html<\/a><\/p><p>\u5206\u7c7b\u67f1\u72b6\u56fe\uff08GO\u5bcc\u96c6\uff09\u7ed8\u56fe\u7f51\u7ad9\u4f7f\u7528\u6559\u7a0b\uff1a<a href=\"https:\/\/www.bilibili.com\/video\/BV1CU4y1w7WM\/\">https:\/\/www.bilibili.com\/video\/BV1CU4y1w7WM\/<\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-6fbcbb7 e-grid 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