{"id":231,"date":"2017-03-12T14:48:00","date_gmt":"2017-03-12T06:48:00","guid":{"rendered":"https:\/\/www.next-bioinfo.tw\/?p=231"},"modified":"2023-09-04T14:50:06","modified_gmt":"2023-09-04T06:50:06","slug":"%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94","status":"publish","type":"post","link":"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/","title":{"rendered":"\u3010NGS \u6b21\u4e16\u4ee3\u57fa\u56e0\u9ad4\u8cc7\u6599\u79d1\u5b78\u3011 \u57fa\u790e\u6559\u5b78 02 \u751f\u8cc7\u5b78\u8853\u7814\u7a76\u6d41\u7a0b\u4e2d\u5e38\u898b\u7684\u7a0b\u5f0f\u5f59\u6574"},"content":{"rendered":"<p>\u9019\u88e1\u6309\u7167\u5e38\u898b\u5f97\u4e0a\u4e0b\u6e38\u5206\u6790\u968e\u6bb5\uff0c\u4ee5\u53ca\u6703\u4f7f\u7528\u5230\u7684\u5de5\u5177\u6574\u7406\u5982\u4e0b\uff0c\u53ef\u4ee5\u6bd4\u8f03\u5feb\u901f\u4e0a\u624b\u6574\u500b\u5206\u6790\u65b9\u6cd5\u3002<\/p>\n\n\n\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_54_1 counter-hierarchy ez-toc-counter ez-toc-grey ez-toc-container-direction\">\n<div class=\"ez-toc-title-container\">\n<p class=\"ez-toc-title\" >Table of Contents<\/p>\n<span class=\"ez-toc-title-toggle\"><a href=\"#\" class=\"ez-toc-pull-right ez-toc-btn ez-toc-btn-xs ez-toc-btn-default ez-toc-toggle\" aria-label=\"Toggle Table of Content\" role=\"button\"><label for=\"item-6a6d40d109c2b\" ><span class=\"\"><span style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #999;color:#999\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewbox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #999;color:#999\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewbox=\"0 0 24 24\" version=\"1.2\" baseprofile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/label><input aria-label=\"Toggle\" type=\"checkbox\"  id=\"item-6a6d40d109c2b\"><\/a><\/span><\/div>\n<nav><ul class='ez-toc-list ez-toc-list-level-1' ><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#FASTQ_%E4%B8%8B%E8%BC%89\" title=\"FASTQ \u4e0b\u8f09\">FASTQ \u4e0b\u8f09<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#FASTQ_%E5%93%81%E8%B3%AA%E6%8E%A7%E5%88%B6%E4%BB%A5%E5%8F%8A_Trimming\" title=\"FASTQ \u54c1\u8cea\u63a7\u5236\u4ee5\u53ca Trimming\">FASTQ \u54c1\u8cea\u63a7\u5236\u4ee5\u53ca Trimming<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%BA%8F%E5%88%97%E6%AF%94%E5%B0%8D_Aligners\" title=\"\u5e8f\u5217\u6bd4\u5c0d Aligners\">\u5e8f\u5217\u6bd4\u5c0d Aligners<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#SAMBAM_%E8%99%95%E7%90%86%E5%B7%A5%E5%85%B7\" title=\"SAM\/BAM \u8655\u7406\u5de5\u5177\">SAM\/BAM \u8655\u7406\u5de5\u5177<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E9%87%8D%E8%A4%87%E6%A8%99%E8%A8%98%E8%88%87%E7%A7%BB%E9%99%A4_Remove_Duplicate\" title=\"\u91cd\u8907\u6a19\u8a18\u8207\u79fb\u9664 Remove Duplicate\">\u91cd\u8907\u6a19\u8a18\u8207\u79fb\u9664 Remove Duplicate<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-6\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%B3%B0%E5%80%BC%E9%91%91%E5%AE%9A_Peak_Calling\" title=\"\u5cf0\u503c\u9451\u5b9a Peak Calling\">\u5cf0\u503c\u9451\u5b9a Peak Calling<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-7\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%AE%9A%E9%87%8F%E5%B7%A5%E5%85%B7_Quantification\" title=\"\u5b9a\u91cf\u5de5\u5177 Quantification\">\u5b9a\u91cf\u5de5\u5177 Quantification<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-8\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%B7%AE%E7%95%B0%E8%A1%A8%E9%81%94%E5%88%86%E6%9E%90%E8%88%87%E6%A0%A1%E6%AD%A3_Differential_Expression_Analysis\" title=\"\u5dee\u7570\u8868\u9054\u5206\u6790\u8207\u6821\u6b63 Differential Expression Analysis\">\u5dee\u7570\u8868\u9054\u5206\u6790\u8207\u6821\u6b63 Differential Expression Analysis<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-9\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%B7%AE%E7%95%B0%E5%B3%B0%E5%80%BC%E5%88%86%E6%9E%90_Peak_Difference\" title=\"\u5dee\u7570\u5cf0\u503c\u5206\u6790 Peak Difference\">\u5dee\u7570\u5cf0\u503c\u5206\u6790 Peak Difference<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-10\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E8%AE%8A%E7%95%B0%E9%91%91%E5%AE%9A_Mutation_Calling\" title=\"\u8b8a\u7570\u9451\u5b9a Mutation Calling \">\u8b8a\u7570\u9451\u5b9a Mutation Calling <\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-11\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E6%8B%B7%E8%B2%9D%E6%95%B8%E8%AE%8A%E7%95%B0%E9%91%91%E5%AE%9A_Copy_number_variation_Calling\" title=\"\u62f7\u8c9d\u6578\u8b8a\u7570\u9451\u5b9a Copy number variation Calling \">\u62f7\u8c9d\u6578\u8b8a\u7570\u9451\u5b9a Copy number variation Calling <\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-12\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%9F%BA%E5%BA%8F%E5%88%86%E6%9E%90_Motif_Analysis\" title=\"\u57fa\u5e8f\u5206\u6790 Motif Analysis \">\u57fa\u5e8f\u5206\u6790 Motif Analysis <\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-13\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%B3%B0%E5%80%BC%E8%A8%BB%E9%87%8B_Peak_Annotation\" title=\"\u5cf0\u503c\u8a3b\u91cb Peak Annotation \">\u5cf0\u503c\u8a3b\u91cb Peak Annotation <\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-14\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%9F%BA%E5%9B%A0%E9%9B%86%E5%AF%8C%E9%9B%86%E5%88%86%E6%9E%90Gene_Set_Enrichment_Analysis\" title=\"\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790Gene Set Enrichment Analysis \">\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790Gene Set Enrichment Analysis <\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-15\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2017\/03\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91-%e5%9f%ba%e7%a4%8e%e6%95%99%e5%ad%b8-02-%e7%94%9f%e8%b3%87%e5%ad%b8%e8%a1%93%e7%a0%94\/#%E5%9F%BA%E5%9B%A0%E6%9C%AC%E9%AB%94%E5%88%86%E6%9E%90%E5%9F%BA%E5%9B%A0%E5%8A%9F%E8%83%BD%E5%88%86%E6%9E%90_Gene_Ontology_analysis\" title=\"\u57fa\u56e0\u672c\u9ad4\u5206\u6790(\u57fa\u56e0\u529f\u80fd\u5206\u6790) Gene Ontology&nbsp; analysis \">\u57fa\u56e0\u672c\u9ad4\u5206\u6790(\u57fa\u56e0\u529f\u80fd\u5206\u6790) Gene Ontology&nbsp; analysis <\/a><\/li><\/ul><\/nav><\/div>\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"FASTQ_%E4%B8%8B%E8%BC%89\"><\/span>FASTQ \u4e0b\u8f09<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>fastq-dump(SRA Tool Kit) : <a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/ncbi\/sra-tools\/wiki\/02.-Installing-SRA-Toolkit\" target=\"_blank\">https:\/\/github.com\/ncbi\/sra-tools\/wiki\/02.-Installing-SRA-Toolkit<\/a><\/li>\n\n\n\n<li>fasterq-dump : <a href=\"https:\/\/github.com\/ncbi\/sra-tools\/wiki\/HowTo:-fasterq-dump\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/github.com\/ncbi\/sra-tools\/wiki\/HowTo:-fasterq-dump<\/a> <\/li>\n\n\n\n<li>parallel-fastq-dump : <a href=\"https:\/\/github.com\/rvalieris\/parallel-fastq-dump\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/github.com\/rvalieris\/parallel-fastq-dump<\/a><\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"FASTQ_%E5%93%81%E8%B3%AA%E6%8E%A7%E5%88%B6%E4%BB%A5%E5%8F%8A_Trimming\"><\/span>FASTQ \u54c1\u8cea\u63a7\u5236\u4ee5\u53ca Trimming<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>fastqc :\n<ul>\n<li> <a rel=\"noreferrer noopener\" href=\"https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/\" target=\"_blank\">https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>fastp : <a href=\"https:\/\/github.com\/OpenGene\/fastp\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/github.com\/OpenGene\/fastp<\/a><\/li>\n\n\n\n<li>Trimmomatic : <a href=\"https:\/\/github.com\/usadellab\/Trimmomatic\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/github.com\/usadellab\/Trimmomatic<\/a><\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%BA%8F%E5%88%97%E6%AF%94%E5%B0%8D_Aligners\"><\/span>\u5e8f\u5217\u6bd4\u5c0d Aligners<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>&nbsp; DNA : Bowtie2 , Bowtie2 , BWA (recommend : BWA-MEM)<\/li>\n\n\n\n<li>&nbsp; RNA : STAR , TopHat , TopHat2<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"SAMBAM_%E8%99%95%E7%90%86%E5%B7%A5%E5%85%B7\"><\/span>SAM\/BAM \u8655\u7406\u5de5\u5177<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>samtools<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E9%87%8D%E8%A4%87%E6%A8%99%E8%A8%98%E8%88%87%E7%A7%BB%E9%99%A4_Remove_Duplicate\"><\/span>\u91cd\u8907\u6a19\u8a18\u8207\u79fb\u9664 Remove Duplicate<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>MarkDuplicates (Picard) <\/li>\n\n\n\n<li> sambamba <\/li>\n\n\n\n<li>samtools<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%B3%B0%E5%80%BC%E9%91%91%E5%AE%9A_Peak_Calling\"><\/span>\u5cf0\u503c\u9451\u5b9a Peak Calling<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>MACS2 <\/li>\n\n\n\n<li>findPeaks(HOMER)<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%AE%9A%E9%87%8F%E5%B7%A5%E5%85%B7_Quantification\"><\/span>\u5b9a\u91cf\u5de5\u5177 Quantification<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>featureCounts (subread)&nbsp; <\/li>\n\n\n\n<li>Cufflinks <\/li>\n\n\n\n<li>htseq-count(HTSeq) <\/li>\n\n\n\n<li>StringTie <\/li>\n\n\n\n<li>RSEM <\/li>\n\n\n\n<li>kallisto(alignment-free)<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%B7%AE%E7%95%B0%E8%A1%A8%E9%81%94%E5%88%86%E6%9E%90%E8%88%87%E6%A0%A1%E6%AD%A3_Differential_Expression_Analysis\"><\/span>\u5dee\u7570\u8868\u9054\u5206\u6790\u8207\u6821\u6b63 Differential Expression Analysis<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>DESeq2 <\/li>\n\n\n\n<li>EdgeR&nbsp; <\/li>\n\n\n\n<li>Limma<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%B7%AE%E7%95%B0%E5%B3%B0%E5%80%BC%E5%88%86%E6%9E%90_Peak_Difference\"><\/span>\u5dee\u7570\u5cf0\u503c\u5206\u6790 Peak Difference<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>DiffBind<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E8%AE%8A%E7%95%B0%E9%91%91%E5%AE%9A_Mutation_Calling\"><\/span>\u8b8a\u7570\u9451\u5b9a Mutation Calling <span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>Mutect2&nbsp; <\/li>\n\n\n\n<li>VarScan&nbsp; <\/li>\n\n\n\n<li>Deepvariant<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E6%8B%B7%E8%B2%9D%E6%95%B8%E8%AE%8A%E7%95%B0%E9%91%91%E5%AE%9A_Copy_number_variation_Calling\"><\/span>\u62f7\u8c9d\u6578\u8b8a\u7570\u9451\u5b9a Copy number variation Calling <span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>CNVseq<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%9F%BA%E5%BA%8F%E5%88%86%E6%9E%90_Motif_Analysis\"><\/span>\u57fa\u5e8f\u5206\u6790 Motif Analysis <span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>HOMER <\/li>\n\n\n\n<li>MEME<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%B3%B0%E5%80%BC%E8%A8%BB%E9%87%8B_Peak_Annotation\"><\/span>\u5cf0\u503c\u8a3b\u91cb Peak Annotation <span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>annotatePeaks (HOMER)<\/li>\n\n\n\n<li>ChIPseeker<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%9F%BA%E5%9B%A0%E9%9B%86%E5%AF%8C%E9%9B%86%E5%88%86%E6%9E%90Gene_Set_Enrichment_Analysis\"><\/span>\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790Gene Set Enrichment Analysis <span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>GSEA&nbsp; and MSigDB <\/li>\n\n\n\n<li>clusterprofiler<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"%E5%9F%BA%E5%9B%A0%E6%9C%AC%E9%AB%94%E5%88%86%E6%9E%90%E5%9F%BA%E5%9B%A0%E5%8A%9F%E8%83%BD%E5%88%86%E6%9E%90_Gene_Ontology_analysis\"><\/span>\u57fa\u56e0\u672c\u9ad4\u5206\u6790(\u57fa\u56e0\u529f\u80fd\u5206\u6790) Gene Ontology&nbsp; analysis <span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<ul>\n<li>Go.db<\/li>\n<\/ul>","protected":false},"excerpt":{"rendered":"<p>\u9019\u88e1\u6309\u7167\u5e38\u898b\u5f97\u4e0a\u4e0b\u6e38\u5206\u6790\u968e\u6bb5\uff0c\u4ee5\u53ca\u6703\u4f7f\u7528\u5230\u7684\u5de5\u5177\u6574\u7406\u5982\u4e0b\uff0c\u53ef\u4ee5\u6bd4\u8f03\u5feb\u901f\u4e0a\u624b\u6574\u500b\u5206\u6790\u65b9\u6cd5\u3002 FASTQ \u4e0b\u8f09 F [&hellip;]<\/p>","protected":false},"author":1,"featured_media":234,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_mi_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"site-container-style":"default","site-container-layout":"default","site-sidebar-layout":"default","site-transparent-header":"default","disable-article-header":"default","disable-site-header":"default","disable-site-footer":"default","disable-content-area-spacing":"default","footnotes":""},"categories":[2],"tags":[12,3,13],"_links":{"self":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/231"}],"collection":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/comments?post=231"}],"version-history":[{"count":2,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/231\/revisions"}],"predecessor-version":[{"id":233,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/231\/revisions\/233"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media\/234"}],"wp:attachment":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media?parent=231"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/categories?post=231"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/tags?post=231"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}