{"id":24112,"date":"2024-01-10T17:26:03","date_gmt":"2024-01-10T09:26:03","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24112"},"modified":"2024-01-10T17:26:05","modified_gmt":"2024-01-10T09:26:05","slug":"%e5%bc%ba%e5%8a%9b%e6%8e%a8%e8%8d%90%ef%bc%81juicer%e5%a4%84%e7%90%86hi-c%e6%95%b0%e6%8d%ae","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24112","title":{"rendered":"\u5f3a\u529b\u63a8\u8350\uff01Juicer\u5904\u7406Hi-C\u6570\u636e"},"content":{"rendered":"\n

Hello\uff0c\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u8ddf\u5927\u5bb6\u89c1\u9762\u5566\uff01<\/p>\n\n\n\n

\u5927\u5bb6\u5bf9Hi-C\u4e86\u89e3\u591a\u5c11\u5462\uff1f\u8fd9\u91cc\u5c0f\u679c\u9996\u5148\u7ed9\u5927\u5bb6\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0bHi-C\u3002Hi-C\u662f\u4e00\u79cd\u7528\u4e8e\u6d4b\u91cf\u57fa\u56e0\u7ec4\u4e2d\u4e0d\u540c\u4f4d\u7f6e\u4e4b\u95f4\u7684\u4e09\u7ef4\u76f8\u4e92\u4f5c\u7528\u7684\u6280\u672f\u3002\u5b83\u53ef\u4ee5\u7528\u4e8e\u7814\u7a76\u57fa\u56e0\u7ec4\u7684\u7ed3\u6784\u548c\u529f\u80fd\uff0c\u6bd4\u5982\u57fa\u56e0\u8c03\u63a7\u3001\u67d3\u8272\u4f53\u57df\u3001\u73af\u72b6\u7ed3\u6784\u7b49\u3002<\/p>\n\n\n\n

Hi-C\u7684\u539f\u7406\u5982\u4e0b\u56fe\u6240\u793a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

Hi-C\u7684\u539f\u7406\u662f\u57fa\u4e8e\u67d3\u8272\u8d28\u8fde\u63a5\u6355\u83b7\uff083C\uff09\u7684\u65b9\u6cd5\uff0c\u5b83\u5229\u7528\u5f62\u5f0f\u7532\u919b\u5c06\u7a7a\u95f4\u4e0a\u76f8\u90bb\u7684\u67d3\u8272\u8d28\u7247\u6bb5\u4ea4\u8054\u8d77\u6765\uff0c\u7136\u540e\u7528\u9650\u5236\u6027\u5185\u5207\u9176\u5c06\u4ea4\u8054\u7684\u67d3\u8272\u8d28\u5207\u5272\u6210\u5c0f\u7247\u6bb5\uff0c\u518d\u7528\u8fde\u63a5\u9176\u5c06\u5207\u5272\u540e\u7684\u7247\u6bb5\u8fde\u63a5\u8d77\u6765\uff0c\u5f62\u6210\u5d4c\u5408\u7684\u8fde\u63a5\u4ea7\u7269\u3002Hi-C\u7684\u7279\u70b9\u662f\u5b83\u53ef\u4ee5\u5168\u9762\u5730\u6d4b\u91cf\u57fa\u56e0\u7ec4\u4e2d\u4efb\u610f\u4e24\u4e2a\u4f4d\u7f6e\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\uff0c\u800c\u4e0d\u662f\u5c40\u9650\u4e8e\u7279\u5b9a\u7684\u533a\u57df\u6216\u76ee\u6807\u3002\u5b83\u901a\u8fc7\u5728\u8fde\u63a5\u5904\u5f15\u5165\u751f\u7269\u7d20\u6807\u8bb0\u7684\u6838\u82f7\u9178\uff0c\u7136\u540e\u7528\u4eb2\u548c\u7eaf\u5316\u7684\u65b9\u6cd5\uff0c\u5c06\u542b\u6709\u8fde\u63a5\u5904\u7684DNA\u7247\u6bb5\u5bcc\u96c6\u5e76\u8fdb\u884c\u6df1\u5ea6\u6d4b\u5e8f\u3002Hi-C\u7684\u7ed3\u679c\u662f\u4e00\u4e2a\u76f8\u4e92\u4f5c\u7528\u77e9\u9635\uff0c\u5176\u4e2d\u6bcf\u4e2a\u5143\u7d20\u8868\u793a\u4e24\u4e2a\u67d3\u8272\u8d28\u7247\u6bb5\u4e4b\u95f4\u7684\u8054\u7cfb\u9891\u7387\uff0c\u4e5f\u5c31\u662f\u5b83\u4eec\u5728\u7a7a\u95f4\u4e0a\u76f8\u4e92\u63a5\u8fd1\u7684\u6982\u7387\u3002\u8054\u7cfb\u9891\u7387\u53ef\u4ee5\u53cd\u6620\u67d3\u8272\u8d28\u7247\u6bb5\u4e4b\u95f4\u7684\u8ddd\u79bb\u548c\u7d27\u5bc6\u7a0b\u5ea6\uff0c\u4ece\u800c\u63ed\u793a\u57fa\u56e0\u7ec4\u7684\u4e09\u7ef4\u7ed3\u6784\u7279\u5f81\u3002<\/p>\n\n\n\n

\u90a3\u4e48\u4eca\u5929\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e00\u4e2a\u5904\u7406Hi-C\u5341\u5206\u65b9\u4fbf\u7684\u8f6f\u4ef6\uff1ajuicer<\/p>\n\n\n\n

juicer\u662f\u4e00\u4e2a\u5904\u7406Hi-C\u6570\u636e\u7684\u8f6f\u4ef6\uff0c\u662f\u4e00\u79cd\u7528\u4e8e\u5206\u6790\u5343\u78b1\u57fa\u5206\u8fa8\u7387\u7684Hi-C\u6570\u636e\u7684\u5e73\u53f0\u3002<\/p>\n\n\n\n

juicer\u5305\u62ec\u4e86\u4e00\u4e2a\u4ecefastq\u539f\u59cb\u6570\u636e\u6587\u4ef6\u751f\u6210Hi-C\u56fe\u7684\u6d41\u7a0b\uff0c\u4ee5\u53ca\u4e00\u4e9b\u7528\u4e8e\u5728Hi-C\u56fe\u4e0a\u8fdb\u884c\u7279\u5f81\u6ce8\u91ca\u7684\u547d\u4ee4\u884c\u5de5\u5177\u3002\u5b83\u53ef\u4ee5\u7528\u4e8e\u7814\u7a76\u57fa\u56e0\u7ec4\u7684\u4e09\u7ef4\u7ed3\u6784\u548c\u529f\u80fd\u3002<\/p>\n\n\n\n

juicer\u7684\u6d41\u7a0b\u4e3b\u8981\u5305\u62ec\u4ee5\u4e0b\u51e0\u4e2a\u6b65\u9aa4\uff1a<\/p>\n\n\n\n

    \n
  1. \u5bf9fastq\u6587\u4ef6\u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u548c\u8fc7\u6ee4\uff0c\u53bb\u9664\u4f4e\u8d28\u91cf\u7684\u8bfb\u6bb5\u548c\u91cd\u590d\u7684\u8bfb\u6bb5\u3002<\/li>\n\n\n\n
  2. \u5bf9\u8fc7\u6ee4\u540e\u7684\u8bfb\u6bb5\u8fdb\u884c\u6bd4\u5bf9\uff0c\u5c06\u5b83\u4eec\u6620\u5c04\u5230\u53c2\u8003\u57fa\u56e0\u7ec4\u4e0a\uff0c\u5e76\u751f\u6210sam\u6216bam\u683c\u5f0f\u7684\u6587\u4ef6\u3002<\/li>\n\n\n\n
  3. \u5bf9\u6bd4\u5bf9\u540e\u7684\u6587\u4ef6\u8fdb\u884c\u540e\u5904\u7406\uff0c\u5c06\u5b83\u4eec\u5206\u5272\u6210\u4e0d\u540c\u7684\u67d3\u8272\u4f53\uff0c\u5e76\u751f\u6210hic\u683c\u5f0f\u7684\u6587\u4ef6\u3002<\/li>\n\n\n\n
  4. \u5bf9hic\u6587\u4ef6\u8fdb\u884c\u5f52\u4e00\u5316\uff0c\u6d88\u9664\u7cfb\u7edf\u6027\u504f\u5dee\uff0c\u5e76\u751f\u6210kr\u6216vc\u683c\u5f0f\u7684\u6587\u4ef6\u3002<\/li>\n\n\n\n
  5. \u5bf9\u5f52\u4e00\u5316\u540e\u7684\u6587\u4ef6\u8fdb\u884c\u5206\u6790\uff0c\u63d0\u53d6\u611f\u5174\u8da3\u7684\u7279\u5f81\uff0c\u6bd4\u5982\u62d3\u6251\u7ed3\u5408\u57df\u3001\u73af\u72b6\u7ed3\u6784\u3001\u76f8\u4e92\u4f5c\u7528\u77e9\u9635\u7b49\u3002<\/li>\n<\/ol>\n\n\n\n

    \u90a3\u4e48\u5c0f\u679c\u6559\u5927\u5bb6\u5982\u4f55\u4f7f\u7528juicer\u53bb\u5904\u7406Hi-C\u6570\u636e\uff0c\u8fd9\u91cc\u5e26\u5927\u5bb6\u751f\u6210hic\u6587\u4ef6\uff0c\u751f\u6210hic\u6587\u4ef6\u4e4b\u540e\u5927\u5bb6\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u60f3\u6cd5\u6765\u505a\u4e00\u4e9b\u5206\u6790\uff0c\u4f8b\u5982AB\u533a\u5ba4\u5212\u5206,TAD\u5206\u6790\u7b49\u3002Juicer\u5b98\u7f51\u533a\u5206\u4e86\u5404\u79cd\u4f7f\u7528\u573a\u666f\uff0c\u8fd9\u91cc\u5c0f\u679c\u5c31\u9ed8\u8ba4\u5927\u5bb6\u662fCPU\u7248\u672c\u4e86\u55f7\uff0c\u8be6\u7ec6\u7684\u7ec6\u8282\u5927\u5bb6\u53ef\u4ee5\u53bb\u770bjuicer\u7684wiki\u55f7\uff1ahttps:\/\/github.com\/aidenlab\/juicer\/wiki<\/a><\/p>\n\n\n\n

    juicer\u7684\u811a\u672c\uff08juicer.sh\uff09\u5927\u6982\u5904\u7406\u6d41\u7a0b\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n\n\n\n

    \u6587\u4ef6\u8f93\u5165->bwa\u6bd4\u5bf9->\u6392\u5e8f->\u5408\u5e76->\u53bb\u9664PCR\u91cd\u590d->\u751f\u6210hic\u6587\u4ef6<\/p>\n\n\n\n

    \u4e0a\u9762\u7684\u6d41\u7a0b\u4e2d\u9700\u8981\u7528\u5230bwa\u6bd4\u5bf9\u8f6f\u4ef6\uff0c\u6240\u4ee5\u6ca1\u5b89\u88c5\u7684\u5c0f\u4f19\u4f34\u8bb0\u5f97\u4f7f\u7528\u4e4b\u524d\u5b89\u88c5bwa\u54e6<\/p>\n\n\n\n

    \u4e0b\u9762\u662f\u5c0f\u679c\u7684\u4ee3\u7801:<\/p>\n\n\n\n

    #\u521b\u5efa\u5de5\u4f5c\u76ee\u5f55\uff0c\u5e76\u4e0b\u8f7djuicer<\/p>\n\n\n\n

    mkdir .\/opt<\/p>\n\n\n\n

    cd opt<\/p>\n\n\n\n

    git clone https:\/\/github.com\/theaidenlab\/juicer.git<\/p>\n\n\n\n

    # \u521b\u5efa\u8f6f\u8fde\u63a5<\/p>\n\n\n\n

    ln -s juicer\/CPU scripts<\/p>\n\n\n\n

    cd scripts\/common<\/p>\n\n\n\n

    wget http:\/\/hicfiles.tc4ga.com.s3.amazonaws.com\/public\/juicer\/juicer_tools.1.7.6_jcuda.0.8.jar<\/p>\n\n\n\n

    ln -s juicer_tools.1.7.6_jcuda.0.8.jar juicer_tools.jar<\/p>\n\n\n\n

    cd ..\/..<\/p>\n\n\n\n

    # \u53c2\u8003\u57fa\u56e0\u7ec4\u5efa\u7acb\u7d22\u5f15\uff0c\u8fd9\u91cc\u5c0f\u679c\u4f7f\u7528\u7684\u662fhg38\u7684\u53c2\u8003\u57fa\u56e0\u7ec4<\/p>\n\n\n\n

    mkdir references<\/p>\n\n\n\n

    cp YOUR_hg38_PATH\/hg38.fasta references\/<\/p>\n\n\n\n

    bwa index hg38.fasta<\/p>\n\n\n\n

    cd ..<\/p>\n\n\n\n

    # \u6dfb\u52a0\u9650\u5236\u6027\u5185\u5207\u9176\u4f4d\u70b9\u4fe1\u606f\uff0c\u5c0f\u4f19\u4f34\u4eec\u6ce8\u610f\u81ea\u5df1\u7684\u662f\u4e0d\u662f MboI \u9176\u54e6<\/p>\n\n\n\n

    mkdir restriction_sites<\/p>\n\n\n\n

    cd restriction_sites\/<\/p>\n\n\n\n

    # \u751f\u6210 hg38_MboI.txt \u6587\u4ef6<\/p>\n\n\n\n

    python ..\/juicer\/misc\/generate_site_positions.py MboI hg38_MboI ..\/references\/hg38.fasta<\/p>\n\n\n\n

    # \u751f\u6210chrom.size\u6587\u4ef6<\/p>\n\n\n\n

    awk ‘BEGIN{OFS=”\\t”}{print $1, $NF}’ hg38_MboI.txt > hg38.chrom.sizes<\/p>\n\n\n\n

    cd ..<\/p>\n\n\n\n

    # \u6dfb\u52a0 fastq \u6587\u4ef6\uff0c\u5c0f\u679c\u91c7\u7528\u662f\u5b98\u65b9\u7684\u6d4b\u8bd5\u6570\u636e\u96c6<\/p>\n\n\n\n

    mkdir fastq && cd fastq<\/p>\n\n\n\n

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

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

    cd ..<\/p>\n\n\n\n

    # \u8fd0\u884c juicer<\/p>\n\n\n\n

    scripts\/juicer.sh -D YOUR_juicer_PATH -y restriction_sites\/hg38_MboI.txt -z references\/hg38.fasta -p restriction_sites\/hg38.chrom.sizes -s MboI<\/p>\n\n\n\n

    \u6700\u540e\u751f\u6210\u7684\u7ed3\u679c\u6587\u4ef6\u751f\u6210\u5728aligned\u6587\u4ef6\u5939\u4e2d\uff0c\u6d41\u7a0b\u4e2d\u751f\u6210\u7684\u6587\u4ef6\u5728splits\u6587\u4ef6\u5939\u4e2d\uff08\u4f8b\u5982\u6bd4\u5bf9\u751f\u6210\u7684sam\u6587\u4ef6\uff09\uff0caligned\u6587\u4ef6\u5939\u4e2d\u4e2d\u5c31\u6709\u5927\u5bb6\u6700\u5173\u6ce8\u7684hic\u6587\u4ef6\u5566\uff0c\u5927\u5bb6\u4ed4\u7ec6\u770b\u4f1a\u53d1\u73b0\u6709\u4e24\u4e2ahic\u6587\u4ef6\uff0c\u5176\u4e2d\u7684inter_30.hic\u662f\u8bbe\u7f6e\u4e86mapQ threshold > 30\u8fc7\u6ee4\u540e\u7684\u7ed3\u679c\u3002<\/p>\n\n\n\n

    hic\u6587\u4ef6\u7684\u683c\u5f0f\u5927\u5bb6\u53ef\u4ee5\u770b\u4e0b\u9762\u7684\u94fe\u63a5\uff1a<\/p>\n\n\n\n

    \nhttps:\/\/github.com\/aidenlab\/hic-format\/blob\/master\/HiCFormatV9.md\n<\/div><\/figure>\n\n\n\n

    \u5c0f\u679c\u7684splits\u6587\u4ef6\u5939\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u5c0f\u679c\u7684aligned\u6587\u4ef6\u5939\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u4eca\u5929\u7684\u5173\u4e8ejuicer\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\n\n

    \u5f3a\u529b\u63a8\u8350\uff01Juicer\u5904\u7406Hi-C\u6570\u636e<\/h1>\n

    Hello\uff0c\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u8ddf\u5927\u5bb6\u89c1\u9762\u5566\uff01<\/p>\n

    \u5927\u5bb6\u5bf9Hi-C\u4e86\u89e3\u591a\u5c11\u5462\uff1f\u8fd9\u91cc\u5c0f\u679c\u9996\u5148\u7ed9\u5927\u5bb6\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0bHi-C\u3002Hi-C\u662f\u4e00\u79cd\u7528\u4e8e\u6d4b\u91cf\u57fa\u56e0\u7ec4\u4e2d\u4e0d\u540c\u4f4d\u7f6e\u4e4b\u95f4\u7684\u4e09\u7ef4\u76f8\u4e92\u4f5c\u7528\u7684\u6280\u672f\u3002\u5b83\u53ef\u4ee5\u7528\u4e8e\u7814\u7a76\u57fa\u56e0\u7ec4\u7684\u7ed3\u6784\u548c\u529f\u80fd\uff0c\u6bd4\u5982\u57fa\u56e0\u8c03\u63a7\u3001\u67d3\u8272\u4f53\u57df\u3001\u73af\u72b6\u7ed3\u6784\u7b49\u3002<\/p>\n

    Hi-C\u7684\u539f\u7406\u5982\u4e0b\u56fe\u6240\u793a<\/p>\n

    <\/p>\n

    Hi-C\u7684\u539f\u7406\u662f\u57fa\u4e8e\u67d3\u8272\u8d28\u8fde\u63a5\u6355\u83b7\uff083C\uff09\u7684\u65b9\u6cd5\uff0c\u5b83\u5229\u7528\u5f62\u5f0f\u7532\u919b\u5c06\u7a7a\u95f4\u4e0a\u76f8\u90bb\u7684\u67d3\u8272\u8d28\u7247\u6bb5\u4ea4\u8054\u8d77\u6765\uff0c\u7136\u540e\u7528\u9650\u5236\u6027\u5185\u5207\u9176\u5c06\u4ea4\u8054\u7684\u67d3\u8272\u8d28\u5207\u5272\u6210\u5c0f\u7247\u6bb5\uff0c\u518d\u7528\u8fde\u63a5\u9176\u5c06\u5207\u5272\u540e\u7684\u7247\u6bb5\u8fde\u63a5\u8d77\u6765\uff0c\u5f62\u6210\u5d4c\u5408\u7684\u8fde\u63a5\u4ea7\u7269\u3002Hi-C\u7684\u7279\u70b9\u662f\u5b83\u53ef\u4ee5\u5168\u9762\u5730\u6d4b\u91cf\u57fa\u56e0\u7ec4\u4e2d\u4efb\u610f\u4e24\u4e2a\u4f4d\u7f6e\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\uff0c\u800c\u4e0d\u662f\u5c40\u9650\u4e8e\u7279\u5b9a\u7684\u533a\u57df\u6216\u76ee\u6807\u3002\u5b83\u901a\u8fc7\u5728\u8fde\u63a5\u5904\u5f15\u5165\u751f\u7269\u7d20\u6807\u8bb0\u7684\u6838\u82f7\u9178\uff0c\u7136\u540e\u7528\u4eb2\u548c\u7eaf\u5316\u7684\u65b9\u6cd5\uff0c\u5c06\u542b\u6709\u8fde\u63a5\u5904\u7684DNA\u7247\u6bb5\u5bcc\u96c6\u5e76\u8fdb\u884c\u6df1\u5ea6\u6d4b\u5e8f\u3002Hi-C\u7684\u7ed3\u679c\u662f\u4e00\u4e2a\u76f8\u4e92\u4f5c\u7528\u77e9\u9635\uff0c\u5176\u4e2d\u6bcf\u4e2a\u5143\u7d20\u8868\u793a\u4e24\u4e2a\u67d3\u8272\u8d28\u7247\u6bb5\u4e4b\u95f4\u7684\u8054\u7cfb\u9891\u7387\uff0c\u4e5f\u5c31\u662f\u5b83\u4eec\u5728\u7a7a\u95f4\u4e0a\u76f8\u4e92\u63a5\u8fd1\u7684\u6982\u7387\u3002\u8054\u7cfb\u9891\u7387\u53ef\u4ee5\u53cd\u6620\u67d3\u8272\u8d28\u7247\u6bb5\u4e4b\u95f4\u7684\u8ddd\u79bb\u548c\u7d27\u5bc6\u7a0b\u5ea6\uff0c\u4ece\u800c\u63ed\u793a\u57fa\u56e0\u7ec4\u7684\u4e09\u7ef4\u7ed3\u6784\u7279\u5f81\u3002<\/p>\n

    \u90a3\u4e48\u4eca\u5929\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e00\u4e2a\u5904\u7406Hi-C\u5341\u5206\u65b9\u4fbf\u7684\u8f6f\u4ef6\uff1ajuicer<\/p>\n

    juicer\u662f\u4e00\u4e2a\u5904\u7406Hi-C\u6570\u636e\u7684\u8f6f\u4ef6\uff0c\u662f\u4e00\u79cd\u7528\u4e8e\u5206\u6790\u5343\u78b1\u57fa\u5206\u8fa8\u7387\u7684Hi-C\u6570\u636e\u7684\u5e73\u53f0\u3002<\/p>\n

    juicer\u5305\u62ec\u4e86\u4e00\u4e2a\u4ecefastq\u539f\u59cb\u6570\u636e\u6587\u4ef6\u751f\u6210Hi-C\u56fe\u7684\u6d41\u7a0b\uff0c\u4ee5\u53ca\u4e00\u4e9b\u7528\u4e8e\u5728Hi-C\u56fe\u4e0a\u8fdb\u884c\u7279\u5f81\u6ce8\u91ca\u7684\u547d\u4ee4\u884c\u5de5\u5177\u3002\u5b83\u53ef\u4ee5\u7528\u4e8e\u7814\u7a76\u57fa\u56e0\u7ec4\u7684\u4e09\u7ef4\u7ed3\u6784\u548c\u529f\u80fd\u3002<\/p>\n

    juicer\u7684\u6d41\u7a0b\u4e3b\u8981\u5305\u62ec\u4ee5\u4e0b\u51e0\u4e2a\u6b65\u9aa4\uff1a<\/p>\n

      \n
    1. \u5bf9fastq\u6587\u4ef6\u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u548c\u8fc7\u6ee4\uff0c\u53bb\u9664\u4f4e\u8d28\u91cf\u7684\u8bfb\u6bb5\u548c\u91cd\u590d\u7684\u8bfb\u6bb5\u3002<\/li>\n
    2. \u5bf9\u8fc7\u6ee4\u540e\u7684\u8bfb\u6bb5\u8fdb\u884c\u6bd4\u5bf9\uff0c\u5c06\u5b83\u4eec\u6620\u5c04\u5230\u53c2\u8003\u57fa\u56e0\u7ec4\u4e0a\uff0c\u5e76\u751f\u6210sam\u6216bam\u683c\u5f0f\u7684\u6587\u4ef6\u3002<\/li>\n
    3. \u5bf9\u6bd4\u5bf9\u540e\u7684\u6587\u4ef6\u8fdb\u884c\u540e\u5904\u7406\uff0c\u5c06\u5b83\u4eec\u5206\u5272\u6210\u4e0d\u540c\u7684\u67d3\u8272\u4f53\uff0c\u5e76\u751f\u6210hic\u683c\u5f0f\u7684\u6587\u4ef6\u3002<\/li>\n
    4. \u5bf9hic\u6587\u4ef6\u8fdb\u884c\u5f52\u4e00\u5316\uff0c\u6d88\u9664\u7cfb\u7edf\u6027\u504f\u5dee\uff0c\u5e76\u751f\u6210kr\u6216vc\u683c\u5f0f\u7684\u6587\u4ef6\u3002<\/li>\n
    5. \u5bf9\u5f52\u4e00\u5316\u540e\u7684\u6587\u4ef6\u8fdb\u884c\u5206\u6790\uff0c\u63d0\u53d6\u611f\u5174\u8da3\u7684\u7279\u5f81\uff0c\u6bd4\u5982\u62d3\u6251\u7ed3\u5408\u57df\u3001\u73af\u72b6\u7ed3\u6784\u3001\u76f8\u4e92\u4f5c\u7528\u77e9\u9635\u7b49\u3002<\/li>\n<\/ol>\n

      \u90a3\u4e48\u5c0f\u679c\u6559\u5927\u5bb6\u5982\u4f55\u4f7f\u7528juicer\u53bb\u5904\u7406Hi-C\u6570\u636e\uff0c\u8fd9\u91cc\u5e26\u5927\u5bb6\u751f\u6210hic\u6587\u4ef6\uff0c\u751f\u6210hic\u6587\u4ef6\u4e4b\u540e\u5927\u5bb6\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u60f3\u6cd5\u6765\u505a\u4e00\u4e9b\u5206\u6790\uff0c\u4f8b\u5982AB\u533a\u5ba4\u5212\u5206,TAD\u5206\u6790\u7b49\u3002Juicer\u5b98\u7f51\u533a\u5206\u4e86\u5404\u79cd\u4f7f\u7528\u573a\u666f\uff0c\u8fd9\u91cc\u5c0f\u679c\u5c31\u9ed8\u8ba4\u5927\u5bb6\u662fCPU\u7248\u672c\u4e86\u55f7\uff0c\u8be6\u7ec6\u7684\u7ec6\u8282\u5927\u5bb6\u53ef\u4ee5\u53bb\u770bjuicer\u7684wiki\u55f7\uff1ahttps:\/\/github.com\/aidenlab\/juicer\/wiki<\/a><\/p>\n

      juicer\u7684\u811a\u672c\uff08juicer.sh\uff09\u5927\u6982\u5904\u7406\u6d41\u7a0b\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

      \u6587\u4ef6\u8f93\u5165->bwa\u6bd4\u5bf9->\u6392\u5e8f->\u5408\u5e76->\u53bb\u9664PCR\u91cd\u590d->\u751f\u6210hic\u6587\u4ef6<\/p>\n

      \u4e0a\u9762\u7684\u6d41\u7a0b\u4e2d\u9700\u8981\u7528\u5230bwa\u6bd4\u5bf9\u8f6f\u4ef6\uff0c\u6240\u4ee5\u6ca1\u5b89\u88c5\u7684\u5c0f\u4f19\u4f34\u8bb0\u5f97\u4f7f\u7528\u4e4b\u524d\u5b89\u88c5bwa\u54e6<\/p>\n

      \u4e0b\u9762\u662f\u5c0f\u679c\u7684\u4ee3\u7801:<\/p>\n

      #\u521b\u5efa\u5de5\u4f5c\u76ee\u5f55\uff0c\u5e76\u4e0b\u8f7djuicer<\/p>\n

      mkdir .\/opt<\/p>\n

      cd opt<\/p>\n

      git clone https:\/\/github.com\/theaidenlab\/juicer.git<\/p>\n

      # \u521b\u5efa\u8f6f\u8fde\u63a5<\/p>\n

      ln -s juicer\/CPU scripts<\/p>\n

      cd scripts\/common<\/p>\n

      wget http:\/\/hicfiles.tc4ga.com.s3.amazonaws.com\/public\/juicer\/juicer_tools.1.7.6_jcuda.0.8.jar<\/p>\n

      ln -s juicer_tools.1.7.6_jcuda.0.8.jar juicer_tools.jar<\/p>\n

      cd ..\/..<\/p>\n

      # \u53c2\u8003\u57fa\u56e0\u7ec4\u5efa\u7acb\u7d22\u5f15\uff0c\u8fd9\u91cc\u5c0f\u679c\u4f7f\u7528\u7684\u662fhg38\u7684\u53c2\u8003\u57fa\u56e0\u7ec4<\/p>\n

      mkdir references<\/p>\n

      cp YOUR_hg38_PATH\/hg38.fasta references\/<\/p>\n

      bwa index hg38.fasta<\/p>\n

      cd ..<\/p>\n

      # \u6dfb\u52a0\u9650\u5236\u6027\u5185\u5207\u9176\u4f4d\u70b9\u4fe1\u606f\uff0c\u5c0f\u4f19\u4f34\u4eec\u6ce8\u610f\u81ea\u5df1\u7684\u662f\u4e0d\u662f MboI \u9176\u54e6<\/p>\n

      mkdir restriction_sites<\/p>\n

      cd restriction_sites\/<\/p>\n

      # \u751f\u6210 hg38_MboI.txt \u6587\u4ef6<\/p>\n

      python ..\/juicer\/misc\/generate_site_positions.py MboI hg38_MboI ..\/references\/hg38.fasta<\/p>\n

      # \u751f\u6210chrom.size\u6587\u4ef6<\/p>\n

      awk ‘BEGIN{OFS=”\\t”}{print $1, $NF}’ hg38_MboI.txt > hg38.chrom.sizes<\/p>\n

      cd ..<\/p>\n

      # \u6dfb\u52a0 fastq \u6587\u4ef6\uff0c\u5c0f\u679c\u91c7\u7528\u662f\u5b98\u65b9\u7684\u6d4b\u8bd5\u6570\u636e\u96c6<\/p>\n

      mkdir fastq && cd fastq<\/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

      cd ..<\/p>\n

      # \u8fd0\u884c juicer<\/p>\n

      scripts\/juicer.sh -D YOUR_juicer_PATH -y restriction_sites\/hg38_MboI.txt -z references\/hg38.fasta -p restriction_sites\/hg38.chrom.sizes -s MboI<\/p>\n

      \u6700\u540e\u751f\u6210\u7684\u7ed3\u679c\u6587\u4ef6\u751f\u6210\u5728aligned\u6587\u4ef6\u5939\u4e2d\uff0c\u6d41\u7a0b\u4e2d\u751f\u6210\u7684\u6587\u4ef6\u5728splits\u6587\u4ef6\u5939\u4e2d\uff08\u4f8b\u5982\u6bd4\u5bf9\u751f\u6210\u7684sam\u6587\u4ef6\uff09\uff0caligned\u6587\u4ef6\u5939\u4e2d\u4e2d\u5c31\u6709\u5927\u5bb6\u6700\u5173\u6ce8\u7684hic\u6587\u4ef6\u5566\uff0c\u5927\u5bb6\u4ed4\u7ec6\u770b\u4f1a\u53d1\u73b0\u6709\u4e24\u4e2ahic\u6587\u4ef6\uff0c\u5176\u4e2d\u7684inter_30.hic\u662f\u8bbe\u7f6e\u4e86mapQ threshold > 30\u8fc7\u6ee4\u540e\u7684\u7ed3\u679c\u3002<\/p>\n

      hic\u6587\u4ef6\u7684\u683c\u5f0f\u5927\u5bb6\u53ef\u4ee5\u770b\u4e0b\u9762\u7684\u94fe\u63a5\uff1a<\/p>\n

      https:\/\/github.com\/aidenlab\/hic-format\/blob\/master\/HiCFormatV9.md<\/a><\/p>\n

      \u5c0f\u679c\u7684splits\u6587\u4ef6\u5939\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

      <\/p>\n

      \u5c0f\u679c\u7684aligned\u6587\u4ef6\u5939\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

      <\/p>\n

      \u4eca\u5929\u7684\u5173\u4e8ejuicer\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>","protected":false},"excerpt":{"rendered":"

      Hello\uff0c\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u8ddf\u5927\u5bb6\u89c1\u9762\u5566\uff01 \u5927\u5bb6\u5bf9Hi-C\u4e86\u89e3\u591a\u5c11\u5462\uff1f\u8fd9\u91cc\u5c0f\u679c\u9996\u5148\u7ed9\u5927\u5bb6\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0bHi-C\u3002H […]<\/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\/24112"}],"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=24112"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24112\/revisions"}],"predecessor-version":[{"id":24116,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24112\/revisions\/24116"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24112"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24112"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24112"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}