{"id":23722,"date":"2024-01-08T17:39:35","date_gmt":"2024-01-08T09:39:35","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23722"},"modified":"2024-01-08T17:39:36","modified_gmt":"2024-01-08T09:39:36","slug":"%e4%b8%a4%e5%88%86%e9%92%9f%ef%bc%81%e6%95%99%e4%bd%a0%e7%94%bb%e5%87%batss%e5%af%8c%e9%9b%86%e7%83%ad%e5%9b%be%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23722","title":{"rendered":"\u4e24\u5206\u949f\uff01\u6559\u4f60\u753b\u51faTSS\u5bcc\u96c6\u70ed\u56fe\uff01"},"content":{"rendered":"

\u5c0f\u679c\u6700\u8fd1\u6c89\u8ff7ATAC-seq\u4e2d\u65e0\u6cd5\u81ea\u62d4\uff0c\u8fd9\u5c31\u5e26\u5927\u5bb6\u6765\u5b66\u4e60\u7ed8\u5236ATAC-seq\u4e2d\u7684TSS\u5bcc\u96c6\u70ed\u56fe\u3002<\/p>\n

\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u7528\u5230\u7684\u8f6f\u4ef6\u662fdeeptools\u3002\u8fd9\u91cc\u5c0f\u679c\u7ed9\u5927\u5bb6\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0bdeeptools\uff1adeeptools \u662f\u4e00\u5957\u57fa\u4e8e python \u5f00\u53d1\u7684\u5de5\u5177\uff0c\u9002\u7528\u4e8e\u6709\u6548\u5904\u7406\u5206\u6790\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6570\u636e\uff0c\u53ef\u7528\u4e8e ChIP-seq, ATAC-seq \u6216 MNase-seq\u3002deeptools \u5305\u542b\u4e86\u591a\u4e2a\u6709\u7528\u7684\u6a21\u5757\uff0c\u53ef\u4ee5\u5904\u7406 BAM \u6587\u4ef6\u6216 bigWig \u6587\u4ef6\uff0c\u8fdb\u884c\u591a\u79cd\u8d28\u91cf\u68c0\u67e5\uff0c\u521b\u5efa\u6807\u51c6\u7684 bedGraph \u548c bigWig \u683c\u5f0f\u7684\u5f52\u4e00\u5316\u8986\u76d6\u5ea6\u6587\u4ef6\uff0c\u5141\u8bb8\u4e0d\u540c\u6587\u4ef6\u4e4b\u95f4\u7684\u6bd4\u8f83\uff08\u4f8b\u5982\uff0c\u5904\u7406\u7ec4\u548c\u5bf9\u7167\u7ec4\uff09\u3002\u6700\u540e\uff0c\u4f7f\u7528\u8fd9\u4e9b\u5f52\u4e00\u5316\u548c\u6807\u51c6\u5316\u7684\u6587\u4ef6\uff0cdeeptools \u53ef\u4ee5\u521b\u5efa\u8bb8\u591a\u9002\u5408\u53d1\u8868\u7684\u53ef\u89c6\u5316\u56fe\u5f62\uff0c\u7528\u4e8e\u8bc6\u522b\u5bcc\u96c6\u533a\u57df\u548c\u8fdb\u884c\u57fa\u56e0\u7ec4\u7684\u529f\u80fd\u6ce8\u91ca\u3002<\/p>\n

\u7b80\u5355\u6765\u8bf4\uff0cDeeptools\u7684\u4e3b\u8981\u7528\u9014\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. \u5904\u7406 bam \u6587\u4ef6 \u6216\u8005 bam \u8f6c\u5316\u7684 bigwig \u6587\u4ef6\uff1b<\/li>\n
  2. \u6570\u636e\u8d28\u91cf\u63a7\u5236\uff1b<\/li>\n
  3. \u4f5c\u56fe\uff0c\u6bd4\u5982\u70ed\u56fe\u3001\u6298\u7ebf\u56fe<\/li>\n<\/ol>\n

    deeptools\u7684\u5b89\u88c5\u5341\u5206\u7b80\u5355\uff0c\u5b83\u7684\u5b89\u88c5\u65b9\u6cd5\u6709\u591a\u79cd\uff0c\u6700\u7b80\u5355\u7684\u4e00\u79cd\u662f\u4f7f\u7528 conda \u547d\u4ee4\uff1a<\/p>\n

    conda install -c bioconda deeptools<\/p>\n

    \u8fd9\u6837\u53ef\u4ee5\u81ea\u52a8\u5b89\u88c5 deeptools \u53ca\u5176\u6240\u6709\u7684 python \u4f9d\u8d56\u9879<\/p>\n

    \u53e6\u4e00\u79cd\u65b9\u6cd5\u662f\u4f7f\u7528 pip \u547d\u4ee4\uff1a<\/p>\n

    pip install deeptools<\/p>\n

    \u8fd9\u6837\u4e5f\u53ef\u4ee5\u81ea\u52a8\u5b89\u88c5 deeptools \u53ca\u5176\u6240\u6709\u7684 python \u4f9d\u8d56\u9879<\/p>\n

    \u8fd9\u91cc\u5c0f\u679c\u8003\u8003\u5c0f\u4f19\u4f34\u4eec\uff0c\u4f60\u4eec\u8fd8\u8bb0\u5f97TSS\u662f\u4ec0\u4e48\u5417\uff1f\u5982\u679c\u4f60\u77e5\u9053\u7684\u8bdd\uff0c\u90a3\u4e48\u5c0f\u679c\u89c9\u5f97\u4f60\u771f\u662f\u6cf0\u9177\u8fa3\uff01<\/p>\n

    \u63ed\u6653\u7b54\u6848\u54af\uff1a<\/p>\n

    TSS \u662f\u8f6c\u5f55\u8d77\u59cb\u4f4d\u70b9\uff08transcription start site\uff09\u7684\u7f29\u5199\uff0c\u662f\u6307\u4e00\u4e2a\u57fa\u56e0\u7684 5\u2019 \u7aef\u8f6c\u5f55\u7684\u7b2c\u4e00\u4e2a\u78b1\u57fa\uff0c\u5b83\u662f\u4e0e\u65b0\u751f RNA \u94fe\u7b2c\u4e00\u4e2a\u6838\u82f7\u9178\u76f8\u5bf9\u5e94 DNA \u94fe\u4e0a\u7684\u78b1\u57fa\uff0c\u901a\u5e38\u4e3a\u4e00\u4e2a\u560c\u5464\uff08A \u6216 G\uff09\u3002TSS \u662f\u57fa\u56e0\u8f6c\u5f55\u7684\u8d77\u70b9\uff0c\u4e5f\u662f\u542f\u52a8\u5b50\u7684\u4e00\u90e8\u5206\u3002\u542f\u52a8\u5b50\u662f\u4e00\u6bb5\u533a\u57df\uff0c\u4e0e RNA \u805a\u5408\u9176\u7ed3\u5408\u5e76\u80fd\u591f\u8d77\u59cb mRNA \u7684\u5408\u6210\u3002TSS \u524d\u5373 5\u2019 \u672b\u7aef\u7684\u5e8f\u5217\u79f0\u4e3a\u4e0a\u6e38\uff0c\u800c\u628a\u5176\u540e\u5373 3\u2019 \u672b\u7aef\u7684\u5e8f\u5217\u79f0\u4e3a\u4e0b\u6e38\u3002<\/p>\n

    Deeptools\u4e0b\u8f7d\u5b8c\u6210\u4e4b\u540e\uff0c\u5c0f\u679c\u5f00\u59cb\u5e26\u5c0f\u4f19\u4f34\u4eec\u753bTSS\u5bcc\u96c6\u56fe\u54af<\/p>\n

    \u9996\u5148\u51c6\u5907bw\u6587\u4ef6,\u5148\u5efa\u7d22\u5f15\uff0c\u7136\u540e\u8f6cbw\uff0c\u7136\u540e\u53d6\u6ce8\u91cabed\u6587\u4ef6\uff0c\u63a5\u7740\u5f62\u6210\u77e9\u9635\u6587\u4ef6\uff0c\u6700\u540e\u7ed8\u5236TSS\u5bcc\u96c6\u56fe<\/p>\n

    \u4e0b\u9762\u662f\u7b2c\u4e00\u6b65\uff1a\u5bf9bam\u6587\u4ef6\u5efa\u7acb\u7d22\u5f15\uff0c\u8f6cbw\u6587\u4ef6<\/p>\n

    samtools index test.bam<\/p>\n

    bamCoverage -b test.bam -o test.bw<\/p>\n

    \u4e0b\u9762\u662f\u83b7\u53d6\u6ce8\u91cabed\u6587\u4ef6\uff0c\u8fd9\u91cc\u9700\u8981\u7528\u5230\u9009\u7528\u7269\u79cd\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6\u55f7<\/p>\n

    awk ‘$3 == “gene”‘ test.gff3 | awk ‘BEGIN{FS=”\\t|=|;”;OFS=”\\t”}{print $1,$4-1,$4}’ > gene.bed<\/p>\n

    \u53c8\u7528\u5230\u4e86\u6211\u4eec\u7684\u8001\u670b\u53cbawk\uff0c\u4e0d\u4f1a\u7684\u5c0f\u4f19\u4f34\u4eec\u8d76\u7d27\u5b66\u8d77\u6765\u5440<\/p>\n

    \u4e0b\u9762\u662f\u5f62\u6210\u77e9\u9635\u6587\u4ef6\uff0c\u7528 ComputeMatrix \u8ba1\u7b97\u5168\u57fa\u56e0\u7ec4\u8303\u56f4\u5185 peaks \u5728\u57fa\u56e0\u7279\u5f81\u7684\u5206\u5e03\u60c5\u51b5\u3002<\/p>\n

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

    computeMatrix reference-point –referencePoint TSS -p 15 -b 10000 -a 10000 -R gene.bed -S test.bw –skipZeros -o test_TSS.gz –outFileSortedRegions test_genes.bed<\/p>\n

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

    reference-point # \u9009\u62e9\u6a21\u5f0f<\/p>\n

    -p 15 # \u7ebf\u7a0b\u6570<\/p>\n

    –referencePoint TSS # \u9009\u62e9\u53c2\u8003\u70b9\uff0c\u8fd8\u53ef\u4ee5\u9009\u62e9TES, center<\/p>\n

    -b 10000 -a 10000 # \u611f\u5174\u8da3\u7684\u533a\u57df\uff0c-b\u4e0a\u6e38\uff0c-a\u4e0b\u6e38<\/p>\n

    -R # \u57fa\u56e0\u6ce8\u91ca\u4fe1\u606f<\/p>\n

    -S # \u63d0\u4f9b\u7684 bigwig \u6587\u4ef6<\/p>\n

    –skipZeros<\/p>\n

    –outFileSortedRegions # \u8f93\u51fa\u7684\u6587\u4ef6\u540d<\/p>\n

    \u4e0b\u9762\u5c31\u662f\u6700\u540e\u4e00\u6b65\u7ed8\u5236\u5bcc\u96c6\u56fe\u5566\uff0c\u5c0f\u679c\u7684\u4ee3\u7801\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

    plotHeatmap -m test_TSS.gz -out test_Heatmap.png<\/p>\n

    \u4e0b\u9762\u5c31\u662f\u5c0f\u679c\u753b\u51fa\u6765\u7684TSS\u5bcc\u96c6\u56fe\u5566\uff0c\u662f\u4e0d\u662f\u5f88\u7f8e\u89c2\u5462\uff1f<\/p>\n

    <\/p>\n

    \u4eca\u5929\u7684TSS\u5bcc\u96c6\u70ed\u56fe\u5b66\u4e60\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u627e\u5c0f\u679c\u8ba8\u8bba\u54e6\uff0c\u6211\u4eec\u660e\u5929\u89c1\u54af~<\/p>\n","protected":false},"excerpt":{"rendered":"

    \u5c0f\u679c\u6700\u8fd1\u6c89\u8ff7ATAC-seq\u4e2d\u65e0\u6cd5\u81ea\u62d4\uff0c\u8fd9\u5c31\u5e26\u5927\u5bb6\u6765\u5b66\u4e60\u7ed8\u5236ATAC-seq\u4e2d\u7684TSS\u5bcc\u96c6\u70ed\u56fe\u3002 \u9996\u5148\uff0c\u6211\u4eec\u9700 […]<\/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\/23722"}],"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=23722"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23722\/revisions"}],"predecessor-version":[{"id":23724,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23722\/revisions\/23724"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23722"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23722"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23722"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}