{"id":24117,"date":"2024-01-10T17:27:00","date_gmt":"2024-01-10T09:27:00","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24117"},"modified":"2024-01-10T17:27:02","modified_gmt":"2024-01-10T09:27:02","slug":"%e4%b8%89%e5%88%86%e9%92%9f%ef%bc%81hic-pro%e5%b8%a6%e4%bd%a0%e8%b7%91%e5%ae%8chi-c%e5%88%86%e6%9e%90%e6%b5%81%e7%a8%8b","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24117","title":{"rendered":"\u4e09\u5206\u949f\uff01HiC-Pro\u5e26\u4f60\u8dd1\u5b8cHi-C\u5206\u6790\u6d41\u7a0b"},"content":{"rendered":"

Hello\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u6765\u5566<\/p>\n

\u5c0f\u679c\u4eca\u5929\u4f7f\u7528HiC-Pro\u7ed9\u5927\u5bb6\u5206\u6790\u4e00\u4e0bHi-C\u7684\u6570\u636e<\/p>\n

\u9996\u5148\u719f\u6089\u4e09\u7ef4\u57fa\u56e0\u7ec4\u7684\u5c0f\u4f19\u4f34\u4eec\u80af\u5b9a\u90fd\u77e5\u9053Hi-C\u6570\u636e\u7684\u5904\u7406\u8f6f\u4ef6\u91cc\u9762HiC-Pro\u548cjuicer\u662f\u6bd4\u8f83\u6d41\u884c\u7684\uff0c\u90a3\u4e48\u8fd9\u4e24\u4e2a\u8f6f\u4ef6\u7684\u533a\u522b\u548c\u4fa7\u91cd\u70b9\u662f\u4ec0\u4e48\u5462\uff1f\u4e14\u542c\u5c0f\u679c\u7ec6\u7ec6\u9053\u6765<\/p>\n

    \n
  1. HiC-Pro\u662f\u4e00\u4e2a\u7075\u6d3b\u548c\u9ad8\u6548\u7684\u7ba1\u9053\uff0c\u53ef\u4ee5\u4ece\u539f\u59cb\u6d4b\u5e8f\u6570\u636e\u5230\u89c4\u8303\u5316\u7684\u8054\u7cfb\u77e9\u9635\u3002\u5b83\u652f\u6301\u591a\u79cd\u9650\u5236\u6027\u9176\u5207\u4f4d\u70b9\uff0c\u53ef\u4ee5\u5e76\u884c\u5904\u7406\u591a\u4e2a\u6837\u672c\uff0c\u53ef\u4ee5\u68c0\u6d4b\u548c\u8fc7\u6ee4PCR\u91cd\u590d\uff0c\u53ef\u4ee5\u751f\u6210\u591a\u79cd\u683c\u5f0f\u7684\u8f93\u51fa\u6587\u4ef6\u3002<\/li>\n
  2. juicer\u7531\u4e24\u90e8\u5206\u7ec4\u6210\uff1a\u4ece\u539f\u59cb\u6570\u636e\u5230\u521b\u5efaHi-C\u6587\u4ef6\u7684pipeline\u548c\u540e\u7eed\u5206\u6790\u5de5\u5177\u3002\u5b83\u53ef\u4ee5\u5904\u7406terabase\u89c4\u6a21\u7684Hi-C\u6570\u636e\u96c6\uff0c\u81ea\u52a8\u6ce8\u91caLoops\u548cDomains\uff0c\u4e0e\u591a\u4e2a\u96c6\u7fa4\u64cd\u4f5c\u7cfb\u7edf\u548cAmazon Web Services\u517c\u5bb9\u3002\u5b83\u8fd8\u53ef\u4ee5\u5229\u7528GPU\u8fdb\u884c\u5cf0\u503c\u8c03\u7528\u3002<\/li>\n
  3. \u4e24\u8005\u7684\u4e3b\u8981\u533a\u522b\u5728\u4e8ejuicer\u63d0\u4f9b\u4e86\u4e00\u4e2a\u4e00\u952e\u5f0f\u7684\u7cfb\u7edf\uff0c\u800cHiC-Pro\u9700\u8981\u7528\u6237\u81ea\u5df1\u914d\u7f6e\u53c2\u6570\u548c\u8fd0\u884c\u6b65\u9aa4\u3002juicer\u8fd8\u63d0\u4f9b\u4e86\u66f4\u591a\u7684\u540e\u7eed\u5206\u6790\u5de5\u5177\uff0c\u59823D-DNA\uff0c\u53ef\u4ee5\u7528\u6765\u8f85\u52a9\u57fa\u56e0\u7ec4\u7ec4\u88c5\u3002HiC-Pro\u652f\u6301\u591a\u79cd\u9650\u5236\u6027\u9176\u5207\u4f4d\u70b9\uff0c\u800cjuicer\u53ea\u652f\u6301HindIII\u548cMboI\u4e24\u79cd\u3002HiC-Pro\u53ef\u4ee5\u751f\u6210\u591a\u79cd\u683c\u5f0f\u7684\u8f93\u51fa\u6587\u4ef6\uff0c\u5982bed, matrix, pairs\u7b49\uff0c\u800cjuicer\u53ea\u751f\u6210hic\u6587\u4ef6\u3002HiC-Pro\u53ef\u4ee5\u8ba9\u7528\u6237\u81ea\u5df1\u914d\u7f6e\u53c2\u6570\u548c\u8fd0\u884c\u6b65\u9aa4\uff0c\u6709\u66f4\u591a\u7684\u7075\u6d3b\u6027\u548c\u53ef\u5b9a\u5236\u6027\uff0c\u800cjuicer\u662f\u4e00\u4e2a\u4e00\u952e\u5f0f\u7684\u7cfb\u7edf\uff0c\u6709\u4e00\u4e9b\u9ed8\u8ba4\u7684\u8bbe\u7f6e\u548c\u9650\u5236\u3002<\/li>\n<\/ol>\n

    \u53ef\u80fd\u6709\u5c0f\u4f19\u4f34\u5bf9\u7b2c\u4e8c\u70b9\u4e2d\u7684terabase\u8868\u793a\u7591\u95ee\uff0c\u4e0d\u77e5\u9053\u662f\u4ec0\u4e48\uff0c\u5176\u5b9eterabase\u662f\u4e00\u4e2a\u8ba1\u91cf\u5355\u4f4d\uff0c\u8868\u793a10\u768412\u6b21\u65b9\u4e2a\u5b57\u8282\uff0c\u4e5f\u5c31\u662f\u4e00\u4e07\u4ebf\u4e2a\u5b57\u8282\u3002\u5b83\u901a\u5e38\u7528\u6765\u8868\u793a\u5927\u89c4\u6a21\u7684\u6570\u636e\u5b58\u50a8\u6216\u4f20\u8f93\u3002\u4f8b\u5982\uff0c\u4e00\u4e2aterabase\u7684Hi-C\u6570\u636e\u96c6\u5c31\u662f\u5305\u542b\u4e86\u4e00\u4e07\u4ebf\u4e2aHi-C\u6d4b\u5e8f\u5bf9\u7684\u6570\u636e\u96c6<\/p>\n

    \u542c\u8bf4HiC-Pro\u8f6f\u4ef6\u5b89\u88c5\u5751\u5f88\u591a\uff1f\u5c0f\u679c\u624b\u628a\u624b\u6559\u5927\u5bb6\u5b89\u88c5HiC-Pro\uff01<\/p>\n

      \n
    1. \u9996\u5148\u521b\u5efa\u81ea\u5df1\u7684\u8f6f\u4ef6\u76ee\u5f55\u7136\u540e\u8fdb\u5165\uff0c\u63a5\u7740\u4e0b\u8f7dHiC-Pro\uff1a<\/li>\n<\/ol>\n

      wget https:\/\/github.com\/nservant\/HiC-Pro\/archive\/refs\/tags\/v3.1.0.tar.gz<\/a><\/p>\n

        \n
      1. \u89e3\u538b\u51fa\u6765\uff1a<\/li>\n<\/ol>\n

        tar -zxvf HiC-Pro-3.1.0.tar.gz<\/p>\n

          \n
        1. \u4f7f\u7528conda\u6839\u636eyml\u6587\u4ef6\u521b\u5efa\u65b0\u7684\u73af\u5883<\/li>\n<\/ol>\n

          conda env create -f YOUR_PATH\/HiC-Pro-3.1.0\/environment.yml -n hicpro<\/p>\n

            \n
          1. \u5207\u6362\u5230hicpro\u73af\u5883\u5e76\u5b89\u88c5HiC-Pro\uff08\u9700\u8981root\u6743\u9650\uff09<\/li>\n<\/ol>\n

            conda activate HiC-Pro<\/p>\n

            make configure<\/p>\n

            make<\/p>\n

            \u8fd9\u6837\u662f\u6700\u9002\u5408\u5c0f\u767d\u540c\u5b66\u7684\u5b89\u88c5\u5566\uff0c\u63a8\u8350\u4f7f\u7528\u5b98\u65b9\u7684yml\u6587\u4ef6\u521b\u5efa\u73af\u5883\uff0c\u5982\u679c\u662f\u81ea\u5df1\u521b\u5efa\u73af\u5883\u4e0b\u8f7d\u4f9d\u8d56\u7684\u8bdd\uff0c\u8bb0\u5f97\u53bb\u4fee\u6539config-install.txt\u6587\u4ef6\u7684\u5730\u5740\u54e6<\/p>\n

            \u4e0b\u9762\u5c0f\u679c\u5f00\u59cb\u5e26\u5927\u5bb6\u4e00\u8d77\u4f7f\u7528HiC-Pro\u6765\u5206\u6790HiC\u6570\u636e\u5566<\/p>\n

            \u9996\u5148\u6211\u4eec\u9700\u8981\u7684\u6587\u4ef6\u662f\u53c2\u8003\u57fa\u56e0\u7ec4\uff0cbowtie2\u8f6f\u4ef6\u5efa\u7acb\u7684\u7d22\u5f15\uff0c\u542b\u6709\u9176\u5207\u7247\u6bb5\u4fe1\u606f\u7684bed\u6587\u4ef6\uff0c\u57fa\u56e0\u7ec4\u5927\u5c0f\u4fe1\u606f\u7684chrom.size\u6587\u4ef6\u4ee5\u53caHi-C\u7684\u6d4b\u5e8f\u6570\u636e\u96c6\uff08\u8fd9\u91cc\u5c0f\u679c\u4f7f\u7528\u6d4b\u8bd5\u6570\u636e\u96c6\uff09<\/p>\n

            \u9996\u5148\u4e0b\u8f7d\u6d4b\u8bd5\u6570\u636e\u96c6\uff1a<\/p>\n

            wget http:\/\/juicerawsmirror.s3.amazonaws.com\/opt\/juicer\/work\/HIC003\/fastq\/HIC003_S2_L001_R1_001.fastq.gz<\/p>\n

            wget http:\/\/juicerawsmirror.s3.amazonaws.com\/opt\/juicer\/work\/HIC003\/fastq\/HIC003_S2_L001_R2_001.fastq.gz<\/p>\n

            \u5c0f\u679c\u53c2\u8003\u57fa\u56e0\u7ec4\u9009\u62e9\u7684\u662fhg38\uff0c\u63a5\u7740\u4f7f\u7528bowtie2-build\u6765\u5efa\u7acb\u7d22\u5f15\uff1a<\/p>\n

            bowtie2-build -f hg38.fasta hg38<\/p>\n

            \u53c2\u6570-f\u6307\u5b9a\u53c2\u8003\u57fa\u56e0\u7ec4\uff0c\u540e\u9762\u662f\u7d22\u5f15\u6587\u4ef6\u7684\u524d\u7f00\uff0c\u6700\u540e\u4f1a\u751f\u62106\u4e2abt2\u6587\u4ef6<\/p>\n

            \u9176\u5207\u7247\u6bb5\u4fe1\u606f\u7684bed\u6587\u4ef6\u4f7f\u7528digest_genome.py\u6765\u751f\u6210\uff0cdigest_genome.py\u811a\u672c\u5728HiC-Pro-3.1.0\/bin\/utils\u76ee\u5f55\u4e0b\u9762\uff1a<\/p>\n

            python3 \/HiC-Pro-3.1.0\/bin\/utils\/digest_genome.py\u00a0 hg38.fasta -r MboI -o hg38_MboI.bed<\/p>\n

            \u53c2\u6570-r\u6307\u5b9a\u9176\u5207\u79cd\u7c7b\uff0c\u4e0d\u533a\u5206\u5927\u5c0f\u5199<\/p>\n

            \u53c2\u6570-o\u6307\u5b9a\u751f\u6210\u6587\u4ef6\u540d\u79f0<\/p>\n

            \u5c0f\u679c\u751f\u6210\u7684hg38_MboI.bed\u6587\u4ef6\u5982\u4e0b\uff1a<\/p>\n

            <\/p>\n

            \u5176\u4e2d\u7b2c\u4e09\u5217\u662f\u68c0\u6d4b\u5230\u7684\u9176\u5207\u4f4d\u70b9\u5bf9\u5e94\u7684\u4f4d\u7f6e<\/p>\n

            \u5c0f\u679c\u4f7f\u7528samtools\u548cawk\u5de5\u5177\u6765\u5f97\u5230chrom.size\u6587\u4ef6\uff1a<\/p>\n

            \u9996\u5148\u4f7f\u7528samtools\u8f6f\u4ef6\u5bf9\u53c2\u8003\u57fa\u56e0\u7ec4\u5efa\u7acb\u7d22\u5f15\uff1a<\/p>\n

            samtools faidx hg38.fasta<\/p>\n

            \u7136\u540e\u4f7f\u7528awk\u6765\u5bf9fai\u6587\u4ef6\u8fdb\u884c\u64cd\u4f5c\uff1a<\/p>\n

            awk ‘{print $1 “\\t” $2}’ hg38.fasta.fai > hg38.chrom.sizes<\/p>\n

            \u4e0a\u9762\u6587\u4ef6\u7684\u51c6\u5907\u5de5\u4f5c\u5df2\u7ecf\u5b8c\u6210\u4e86\uff0c\u4e0b\u9762\u5f00\u59cb\u4f7f\u7528HiC-Pro\u8f6f\u4ef6\u8fdb\u884c\u5206\u6790\u4e86<\/p>\n

            \u4e0d\u8fc7\u6211\u4eec\u9996\u5148\u8981\u5728HiC-Pro\u7684\u8f6f\u4ef6\u6839\u76ee\u5f55\u4e0b\u521b\u5efa\u4e00\u4e2arawdata\u6587\u4ef6\u5939\u6765\u5b58\u653e\u6211\u4eec\u7684\u6d4b\u5e8f\u6570\u636e\uff0c<\/p>\n

            \u4e0b\u9762\u6211\u4eec\u8981\u4fee\u6539\u914d\u7f6e\u6587\u4ef6\uff1aconfig-hicpro.txt\uff0c\u4e0b\u9762\u662f\u4e00\u4e9b\u91cd\u8981\u7684\u8bbe\u7f6e\u53c2\u6570\uff1a<\/p>\n

              \n
            1. N_CPU\uff0cCPU\u6570\u76ee\uff1b<\/li>\n
            2. BOWTIE2_IDX_PATH\uff0c\u7d22\u5f15\u6240\u5728\u76ee\u5f55<\/li>\n
            3. REFERENCE_GENOME\uff0c\u6bd4\u5bf9\u53c2\u8003\u57fa\u56e0\u7ec4\u8def\u5f84\u53ca\u524d\u7f00<\/li>\n
            4. GENOME_SIZE\uff0cchrom.sizes\u6587\u4ef6\u7684\u8def\u5f84<\/li>\n
            5. GENOME_FRAGMENT\uff0c\u9176\u5207\u7247\u6bb5\u7684bed\u6587\u4ef6\u7684\u8def\u5f84<\/li>\n
            6. LIGATION_SITE\uff0c\u9176\u5207\u4f4d\u70b9\u672b\u7aef\u8865\u5e73\u518d\u6b21\u8fde\u63a5\u540e\u5f62\u6210\u7684\u5d4c\u5408\u5e8f\u5217\uff0c\u4f8b\u5982HindIII\uff0c\u5219\u4e3aAAGCTAGCTT\uff1b\u5982\u679c\u662fMboI\u5219\u5e8f\u5217\u4e3aGATCGATC\uff1b<\/li>\n<\/ol>\n

              \u914d\u7f6e\u597d\u6587\u4ef6\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u8dd1\u8d77\u6765\u5566<\/p>\n

              \u5c0f\u679c\u7684\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

              YOUR_PATH\/bin\/HiC-Pro -c YOUR_PATH\/config-hicpro.txt -i YOUR_PATH\/rawdata\/ -o YOUR_PATH\/test_re<\/p>\n

              \u5176\u4e2d\uff0c-c\u53c2\u6570\u6307\u5b9a\u914d\u7f6e\u6587\u4ef6\uff0c-i\u6307\u5b9a\u6570\u636e\u7684\u8def\u5f84\uff0c-o\u6307\u5b9a\u751f\u6210\u6587\u4ef6\u5939\u7684\u8def\u5f84<\/p>\n

              <\/p>\n

              \u751f\u6210\u7684\u65e5\u5fd7\u6587\u4ef6\u5728-o\u6307\u5b9a\u7684\u6587\u4ef6\u5939\u91cc\u9762<\/p>\n

              \u4e0b\u9762\u662f\u5c0f\u679c\u7684\u7ed3\u679c\u6587\u4ef6\uff1a<\/p>\n

              <\/p>\n

              \u5176\u4e2d\uff0cbowtie_results:\u6bd4\u5bf9\u7ed3\u679c\u6240\u5728\u76ee\u5f55\uff1b<\/p>\n

              hic_results:hic\u77e9\u9635\u53ca\u5206\u6790\u7ed3\u679c\u6240\u5728\u76ee\u5f55\uff1b<\/p>\n

              logs:\u5b58\u653e\u5206\u6790\u65e5\u5fd7\uff1b<\/p>\n

              rawdata\uff1a\u94fe\u63a5\u4e86\u539f\u59cb\u6570\u636e\uff1b<\/p>\n

              tmp\uff1a\u5b58\u653e\u4e2d\u95f4\u6587\u4ef6<\/p>\n

              \u76ee\u5f55bowtie_results\u4e0b\u5171\u6709\u4e09\u4e2a\u6587\u4ef6\u5939\uff1a<\/p>\n

              <\/p>\n

                \n
              1. bwt2\uff1a\u5b58\u653e\u5408\u5e76\u540e\u7684bam\u6587\u4ef6\u548c\u7edf\u8ba1\u7ed3\u679c<\/li>\n
              2. bwt2_global\uff1a\u5b58\u653e\u5168\u5c40\u6bd4\u5bf9\u7ed3\u679c<\/li>\n
              3. bwt2_local\uff1a\u5b58\u653e\u5c40\u90e8\u6bd4\u5bf9\u7ed3\u679c<\/li>\n<\/ol>\n

                \u76ee\u5f55hic_results\u4e0b\u9762\u6709\u56db\u4e2a\u6587\u4ef6\u5939\uff1a<\/p>\n

                <\/p>\n

                  \n
                1. data\uff1a\u5b58\u653evalid pair reads\u53ca\u5176\u4ed6\u6570\u636e\u6587\u4ef6<\/li>\n
                2. matrix\uff1a\u5b58\u653e\u4e0d\u540c\u5206\u8fa8\u7387\u77e9\u9635\u6587\u4ef6<\/li>\n
                3. pic\uff1a\u5b58\u653e\u7edf\u8ba1\u5206\u6790\u56fe\u7247<\/li>\n
                4. stats\uff1a\u5b58\u653e\u7edf\u8ba1\u8868<\/li>\n<\/ol>\n

                  \u4eca\u5929\u7684\u5173\u4e8eHiC-Pro\u8f6f\u4ef6\u7684\u5b66\u4e60\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u627e\u5c0f\u679c\u8ba8\u8bba\uff0c\u6709\u611f\u89c9\u751f\u4fe1\u5206\u6790\u590d\u6742\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528\u6211\u4eec\u7684\u751f\u4fe1\u5c0f\u5de5\u5177\u54e6\uff0c\u94fe\u63a5\u5728\u8fd9\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/a>\uff0c\u6211\u4eec\u660e\u5929\u89c1\u54af~<\/p>\n","protected":false},"excerpt":{"rendered":"

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