{"id":24074,"date":"2024-01-10T17:14:16","date_gmt":"2024-01-10T09:14:16","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24074"},"modified":"2024-01-10T17:14:17","modified_gmt":"2024-01-10T09:14:17","slug":"%e4%b8%89%e5%88%86%e9%92%9f%ef%bc%81%e5%b0%8f%e6%9e%9c%e5%b8%a6%e4%bd%a0%e8%8e%b7%e5%be%97hi-c%e7%9a%84contact%e7%9f%a9%e9%98%b5%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24074","title":{"rendered":"\u4e09\u5206\u949f\uff01\u5c0f\u679c\u5e26\u4f60\u83b7\u5f97Hi-C\u7684contact\u77e9\u9635\uff01"},"content":{"rendered":"

\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u6765\u5566\uff01\u8fd9\u6b21\u5e26\u5927\u5bb6\u8fc7\u4e00\u4e0bHi-C\u7684\u6570\u636e\u5206\u6790\u6d41\u7a0b<\/p>\n

<\/p>\n

\u4e0a\u56fe\u662fHi-C\u6d4b\u5e8f\u7684\u539f\u7406\u56fe\uff0c\u5927\u6982\u53ef\u4ee5\u5206\u4e3a\u4e00\u4e0b\u51e0\u6b65\uff1a<\/p>\n

    \n
  1. \u5229\u7528\u7532\u919b\u56fa\u5b9a\u7ec6\u80de\uff0c\u4f7f\u5f97\u86cb\u767d\u8d28\u548cDNA\u56fa\u5b9a\uff0c\u86cb\u767d\u4e0e\u86cb\u767d\u4e4b\u95f4\u8fdb\u884c\u4ea4\u8054<\/li>\n
  2. \u8fdb\u884c\u9176\u5207\uff08HindIII\uff09\uff0c\u4f7f\u5f97\u4ea4\u8054\u4e24\u4fa7\u4ea7\u751f\u7c98\u6027\u672b\u7aef<\/li>\n
  3. \u672b\u7aef\u4fee\u590d\uff0c\u5f15\u5165\u751f\u7269\u7d20\u6807\u8bb0\uff0c\u4f7f\u7528DNA\u8fde\u63a5\u9176\u8fde\u63a5\u4e34\u8fd1\u7684DNA\u7247\u6bb5<\/li>\n
  4. \u86cb\u767d\u9176\u6d88\u5316\u89e3\u9664\u4ea4\u8054\uff0c\u7eaf\u5316DNA\u5e76\u968f\u673a\u6253\u65ad\uff0c\u4eb2\u548c\u7d20\u78c1\u73e0\u6355\u83b7\u5e26\u6709\u751f\u7269\u7d20\u6807\u8bb0\u7684\u7247\u6bb5\uff0c\u8fdb\u884c\u5efa\u5e93<\/li>\n
  5. \u8fdb\u884c\u9ad8\u901a\u91cf\u6d4b\u5e8f<\/li>\n<\/ol>\n

    \u539f\u7406\u61c2\u4e86\uff0c\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u5f00\u59cb\u8d70\u6d41\u7a0b\u54af<\/p>\n

    \u9996\u5148\u662f\u4e0b\u8f7d\u6d4b\u8bd5\u6570\u636e\u96c6\uff08\u53c2\u8003\u57fa\u56e0\u7ec4\u548cHi-C\u6570\u636e\uff09\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    wget https:\/\/s3.amazonaws.com\/4dn-dcic-public\/hic-data-analysis-bootcamp\/input_R1.fastq.gz<\/p>\n

    wget https:\/\/s3.amazonaws.com\/4dn-dcic-public\/hic-data-analysis-bootcamp\/input_R2.fastq.gz<\/p>\n

    gunzip input_R1.fastq.gz<\/p>\n

    gunzip input_R2.fastq.gz<\/p>\n

    # bwa genome index<\/p>\n

    wget https:\/\/s3.amazonaws.com\/4dn-dcic-public\/hic-data-analysis-bootcamp\/hg38.bwaIndex.tgz<\/p>\n

    tar -xzf hg38.bwaIndex.tgz<\/p>\n

    rm hg38.bwaIndex.tgz<\/p>\n

    # chromsizes<\/p>\n

    wget https:\/\/s3.amazonaws.com\/4dn-dcic-public\/hic-data-analysis-bootcamp\/hg38.mainonly.chrom.size<\/p>\n

    \u7ecf\u8fc7\u4e0a\u9762\u7684\u4e0b\u8f7d\uff0c\u53ef\u4ee5\u5f97\u5230\u4e24\u4e2afastq\u6587\u4ef6\u548c\u53c2\u8003\u57fa\u56e0\u7ec4\u6587\u4ef6\u8fd8\u6709\u53c2\u8003\u57fa\u56e0\u7ec4\u7684chrom size \u6587\u4ef6<\/p>\n

    \u4e0b\u9762\u5c31\u5f00\u59cb\u7b2c\u4e00\u6b65\uff1amapping<\/p>\n

    \u4f7f\u7528bwa\u8f6f\u4ef6\u6bd4\u5bf9\u63a5\u7740\u4f7f\u7528samtools\u5c06\u6bd4\u5bf9\u540e\u7684sam\u6587\u4ef6\u8f6c\u6362\u4e3abam\u6587\u4ef6\uff0c\u5c0f\u679c\u7684\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    bwa mem -SP5M -t 32 hg38.fasta input_R1.fastq input_R2.fastq | samtools view -bhS – > output.bam<\/p>\n

    \u4e0b\u9762\u662f\u53c2\u6570\u7684\u89e3\u91ca\uff1a<\/p>\n

    -t \uff1a \u8fdb\u7a0b\u6570<\/p>\n

    -SP5M \uff1aHi-C specific options<\/p>\n

    \u6bd4\u5bf9\u4e4b\u540e\u53ef\u4ee5\u4f7f\u7528samtools view \u7ed3\u5408less\u547d\u4ee4\u6765\u89c2\u5bdf\u751f\u6210\u7684bam\u6587\u4ef6\uff1a
    \nsamtools view out.bam | less -S<\/p>\n

    \u63a5\u7740\u662f\u7b2c\u4e8c\u6b65\u8fc7\u6ee4\uff0c\u5728\u5b9e\u9645\u7684\u6bd4\u5bf9\u4e2d\uff0c\u53ef\u80fd\u53ea\u6709\u4e00\u7aef\u80fd\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u4e0a\uff0c\u53e6\u4e00\u7aef\u65e0\u6cd5\u8bc6\u522b\u5230\u57fa\u56e0\u7ec4\u4e0a\uff0c\u8fd9\u79cd\u60c5\u51b5\u5f52\u4e3aSingleton\uff0c\u5982\u679c\u4e24\u4fa7\u6570\u636e\u90fd\u80fd\u591f\u552f\u4e00\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u4e0a\uff0c\u5219\u5f52\u7c7b\u4e3aUnique mapped reads \uff0c\u5bf9\u4e8e\u52a8\u7269\u57fa\u56e0\u7ec4\uff0cunique mapped reads\u5360\u6d4b\u5e8f\u91cf50%\u4ee5\u4e0a\u53ef\u4ee5\u63a5\u53d7\u3002\u5bf9\u4e8e\u690d\u7269\u6837\u672c\uff0c\u5c24\u5176\u662f\u91cd\u590d\u5e8f\u5217\u8f83\u591a\u7684\u6837\u672c\uff0cUnique mapped reads\u6bd4\u4f8b\u53ef\u80fd\u6025\u5267\u964d\u4f4e\u3002\u5728\u83b7\u53d6Unique mapped reads \u4e4b\u540e\uff0c\u8981\u8fdb\u884c\u8fdb\u4e00\u6b65\u8fc7\u6ee4\u6765\u7b5b\u9009vaild pairs\u3002<\/p>\n

    \u6839\u636eHi-C\u7684\u539f\u7406\uff0c\u4ec5\u5f53\u4e24\u4e2aread\u6765\u6e90\u4e8e\u4e0d\u540c\u7684\u9176\u5207\u7247\u6bb5\u65f6\u624d\u88ab\u8ba4\u4e3a\u662f\u6807\u51c6\u7684\u6587\u5e93\u7247\u6bb5\u3002\u5373\u4e24\u4e2aread\u5206\u522b\u5339\u914d\u5230\u4e0d\u540c\u7684\u9176\u5207\u7247\u6bb5\u4e0a\uff0c\u4e14\u5b9e\u9645\u7247\u6bb5\u5927\u5c0f\u7b26\u5408\u7406\u8bba\u7684\u7247\u6bb5\u5927\u5c0f\uff0c\u8fd9\u6837\u624d\u4f1a\u5c06\u8be5reads\u5f52\u7c7b\u5230vaild pairs\u4e2d<\/p>\n

    \u8fc7\u6ee4\u6b65\u9aa4\u4f7f\u7528\u7684\u8f6f\u4ef6pairtools\uff0c\u4e3b\u8981\u662f\u751f\u6210.pairs\u6587\u4ef6\uff08\u5177\u4f53.pairs\u683c\u5f0f\u53ef\u4ee5\u770b\u8fd9\u4e2a\u94fe\u63a5\uff1ahttps:\/\/github.com\/4dn-dcic\/pairix\/blob\/master\/pairs_format_specification.md<\/a>\uff09\u3002\u5c0f\u679c\u7684\u4ee3\u7801\u5982\u4e0b<\/p>\n

      \n
    1. samtools view -h output.bam | pairtools parse -c hg38.mainonly.chrom.size -o parsed.pairsam<\/li>\n
    2. pairtools sort –nproc 8 -o sorted.parsed.pairsam parsed.pairsam<\/li>\n
    3. less -S sorted.parsed.pairsam<\/li>\n<\/ol>\n

      \u4e0b\u9762\u7684\u6b65\u9aa4\u662f\u53bb\u91cd\uff0c\u53bb\u91cd\u4f7f\u7528\u5230\u7684\u8f6f\u4ef6\u4ecd\u7136\u662fpairtools\uff0c\u5c0f\u679c\u7684\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

      pairtools dedup –mark-dups -o deduped.sorted.parsed.pairsam sorted.parsed.pairsam<\/p>\n

      \u63a5\u7740\u4e0b\u4e00\u4e2a\u6b65\u9aa4\u662fselect\uff0c\u5373\u6839\u636epairs\u7684\u7c7b\u578b\u7b5b\u9009pairs\uff0c\u5177\u4f53\u7684pairs\u7c7b\u578b\u53ef\u4ee5\u53bb\u770bpairtools\u7684\u5b98\u7f51\u55f7<\/p>\n

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

      pairtools select ‘(pair_type == “UU”) or (pair_type == “UR”) or (pair_type ==”RU”) ‘ -o filtered.deduped.sorted.parsed.pairsam deduped.sorted.parsed.pairsam<\/p>\n

      \u4e0a\u8ff0\u4ee3\u7801\u7b5b\u9009\u51faUU\uff0cUR\u548cRU\u7c7b\u578b\u7684pairs<\/p>\n

      \u4e0b\u4e00\u4e2a\u6b65\u9aa4\u662f\u62c6\u5206\u6587\u4ef6\uff1a\u5c06\u6700\u7ec8\u5f97\u5230\u7684.pairsam\u6587\u4ef6\u62c6\u6210.pairs\u6587\u4ef6\u548c.sam\u6587\u4ef6\uff0c\u4f7f\u7528\u5230\u7684\u8f6f\u4ef6\u8fd8\u662f\u8001\u670b\u53cbpairtools\uff01<\/p>\n

      \u5c0f\u679c\u7684\u4ee3\u7801\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

      pairtools split –output-pairs output.pairs filtered.deduped.sorted.parsed.pairsam<\/p>\n

      less -S output.pairs<\/p>\n

      \u8fd9\u662f\u5c0f\u679c\u7684output.pairs\u6587\u4ef6\u7684\u6837\u5b50<\/p>\n

      <\/p>\n

      \u5feb\u7ed3\u675f\u5566\uff0c\u5927\u5bb6\u4e0d\u8981\u7740\u6025\u55f7<\/p>\n

      \u4e0b\u9762\u5c31\u662f\u521b\u5efa\u7d22\u5f15\u5566\uff1a\u5bf9pairs\u6587\u4ef6\u521b\u5efa\u7d22\u5f15\uff0c\u8fd9\u4e2a\u6b65\u9aa4\u7528\u5230\u7684\u8f6f\u4ef6\u662fpairix<\/p>\n

      \u4e0b\u9762\u662f\u5c0f\u679c\u7684\u4ee3\u7801\uff1a<\/p>\n

        \n
      1. \u5bf9.pairs\u6587\u4ef6\u8fdb\u884c\u538b\u7f29\uff0c\u5f97\u5230gz\u6587\u4ef6<\/li>\n<\/ol>\n

        bgzip output.pairs<\/p>\n

          \n
        1. \u4f7f\u7528pairix\u5efa\u7acb\u7d22\u5f15<\/li>\n<\/ol>\n

          pairix -f output.pairs.gz<\/p>\n

            \n
          1. \u67e5\u8be2\u67d3\u8272\u4f53\u67d0\u533a\u57df\u7684\u7684pairs<\/li>\n<\/ol>\n

            pairs pairix output.pairs.gz ‘chr2:3000000-600000000 | chr4:200-400000000’<\/p>\n

            \u4e0b\u9762\u662f\u7b2c\u4e09\u6b65\u7684\u8fd0\u884c\u7ed3\u679c<\/p>\n

            <\/p>\n

            \u4e0b\u4e00\u6b65\u5c31\u662f\u751f\u6210contact\u77e9\u9635\uff0c\u8981\u7528\u5230\u7684\u8f6f\u4ef6\u662fcooler\uff0c\u5927\u5bb6\u4f7f\u7528conda\u5b89\u88c5\u5373\u53ef\u3002\u8f93\u5165\u6587\u4ef6\u662f.pairs\u6587\u4ef6\u548cchromesize\u6587\u4ef6\uff0c\u8f93\u51fa\u5219\u662fcool\u6587\u4ef6<\/p>\n

            \u5c0f\u679c\u7684\u4ee3\u7801\u662f\u8fd9\u6837\u6ef4\uff1a<\/p>\n

            cooler cload pairix hg38.mainonly.chrom.size:50000 output.pairs.gz output.cool<\/p>\n

            \u5176\u4e2dchromesize\u6587\u4ef6\u540e\u7684\uff1a50000 \u662f\u6307bin\uff08\u4e92\u4f5c\u57fa\u672c\u5355\u4f4d\uff09\u4e3a50000<\/p>\n

            \u53ef\u4ee5\u4f7f\u7528\u4e0b\u9762\u547d\u4ee4\u67e5\u770b.cool\u6587\u4ef6\uff08contact\u77e9\u9635\uff09<\/p>\n

            cooler dump -t pixels –header –join -r chr19 output.cool<\/p>\n

            \u5c0f\u679c\u751f\u6210\u7684contact\u77e9\u9635\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/p>\n

            <\/p>\n

            \u4eca\u5929\u7684\u5173\u4e8eHi-C\u5206\u6790\u6d41\u7a0b\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":"

            \u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u6765\u5566\uff01\u8fd9\u6b21\u5e26\u5927\u5bb6\u8fc7\u4e00\u4e0bHi-C\u7684\u6570\u636e\u5206\u6790\u6d41\u7a0b \u4e0a\u56fe\u662fHi-C\u6d4b\u5e8f\u7684\u539f\u7406\u56fe\uff0c\u5927\u6982\u53ef\u4ee5\u5206\u4e3a\u4e00\u4e0b\u51e0\u6b65\uff1a […]<\/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\/24074"}],"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=24074"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24074\/revisions"}],"predecessor-version":[{"id":24081,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24074\/revisions\/24081"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24074"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24074"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24074"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}