{"id":655,"date":"2021-01-06T11:33:54","date_gmt":"2021-01-06T03:33:54","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=655"},"modified":"2021-01-06T11:36:52","modified_gmt":"2021-01-06T03:36:52","slug":"atac-seq%e5%88%86%e6%9e%90%e6%b5%81%e7%a8%8b%ef%bc%88%e4%b8%89%ef%bc%89","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=655","title":{"rendered":"ATAC-seq\u5206\u6790\u6d41\u7a0b\uff08\u4e09\uff09"},"content":{"rendered":"<p>\u524d\u8fb9\u4ecb\u7ecd\u4e86\u4f7f\u7528DiffBind\u8fdb\u884cATAC-seq\u6570\u636e\u7684\u5dee\u5f02\u5206\u6790\uff0cDiffBind\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u65f6\u8c03\u7528\u4e86edgeR\u6216\u8005DESeq2\u5305\uff1b\u76f8\u5bf9\u4e8eDiffBind\u6d41\u7a0b\u6211\u66f4\u4e60\u60ef\u666e\u901a\u8f6c\u5f55\u7ec4\u5206\u6790\u6d41\u7a0b\uff0c\u56e0\u4e3a\u4e24\u8005\u672c\u8d28\u4e0a\u662f\u4e00\u6837\u7684\uff0c\u533a\u522b\u5728\u4e8eATAC-seq\u8981\u6839\u636e\u7ed3\u679c\u7684peak\u6587\u4ef6\u81ea\u5df1\u5236\u5907gtf\u6587\u4ef6\uff0cpeak\u5bf9\u5e94\u7684gtf\u6587\u4ef6\u548cgene\u662f\u4e0d\u4e00\u6837\u7684\uff0c\u4e0d\u540c\u6837\u672c\u95f4\u4e5f\u53ef\u80fd\u5b58\u5728\u5dee\u5f02\u3002<\/p>\n<pre>\r\ncat *.narrowPeak > merged.peaks\r\nsort -k1,1 -k2,2n merged.peaks > merged.peaks.sorted\r\nbedtools merge -i merged.peaks.sorted > bedtools.merged.sorted.bed\r\nawk -v var=ATAC_seq '{print $1\"\\t\"var\"\\texon\\t\"$2\"\\t\"$3\"\\t.\\t+\\t.\\tgene_id \\\"peak_\"NR\"\\\"; transcript_id \\\"peak_\"NR\"\\\";\"}' bedtools.merged.sorted.bed > bedtools.merged.atac.gtf\r\nfeatureCounts -T 18 -p -t exon -g gene_id -a bedtools.merged.atac.gtf -o ATAC_counts.txt *last.bam\r\nsed 1d ATAC_counts.txt | cut -f 1,7-15 > rawATAC_counts.matrix\r\n<\/pre>\n<p>\u4e00\u4e2apeak\u76f8\u5f53\u4e8e\u4e00\u4e2agene\uff0c\u5f97\u5230\u7684\u539f\u59cb\u77e9\u9635\u53ef\u4ee5\u4f7f\u7528DESeq2\u5305\u5206\u6790\uff0c\u7b5b\u9009\u51fa\u5171\u6709\u7279\u6709\u6216\u8005\u5dee\u5f02\u7684peaks\u7b49\u8fdb\u884cpeaks\u7684\u6ce8\u91ca\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u524d\u8fb9\u4ecb\u7ecd\u4e86\u4f7f\u7528DiffBind\u8fdb\u884cATAC-seq\u6570\u636e\u7684\u5dee\u5f02\u5206\u6790\uff0cDiffBind\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u65f6\u8c03\u7528\u4e86edgeR\u6216\u8005DESeq2\u5305\uff1b\u76f8\u5bf9\u4e8eDiffBind\u6d41\u7a0b\u6211\u66f4\u4e60\u60ef\u666e\u901a\u8f6c\u5f55\u7ec4\u5206\u6790\u6d41\u7a0b\uff0c\u56e0\u4e3a\u4e24\u8005\u672c\u8d28\u4e0a\u662f\u4e00\u6837\u7684\uff0c\u533a\u522b\u5728\u4e8eATAC-seq\u8981\u6839\u636e\u7ed3\u679c\u7684peak\u6587\u4ef6\u81ea\u5df1\u5236\u5907gtf\u6587\u4ef6\uff0cpeak\u5bf9\u5e94\u7684gtf\u6587\u4ef6\u548cgene\u662f\u4e0d\u4e00\u6837\u7684\uff0c\u4e0d\u540c\u6837\u672c\u95f4\u4e5f\u53ef\u80fd\u5b58\u5728\u5dee\u5f02\u3002 cat *.narrowPeak > merged.peaks sort -k1,1 -k2,2n merged.peaks > merged.peaks.sorted bedtools merge -i merged.peaks.sorted > bedtools.merged.sorted.bed awk -v var=ATAC_seq &#8216;{print $1&#8243;\\t&#8221;var&#8221;\\texon\\t&#8221;$2&#8243;\\t&#8221;$3&#8243;\\t.\\t+\\t.\\tgene_id \\&#8221;peak_&#8221;NR&#8221;\\&#8221;; transcript_id \\&#8221;peak_&#8221;NR&#8221;\\&#8221;;&#8221;}&#8217; bedtools.merged.sorted.bed > bedtools.merged.atac.gtf featureCounts -T 18 -p -t exon -g gene_id -a bedtools.merged.atac.gtf -o ATAC_counts.txt *last.bam sed 1d ATAC_counts.txt | cut -f 1,7-15 > rawATAC_counts.matrix \u4e00\u4e2apeak\u76f8\u5f53\u4e8e\u4e00\u4e2agene\uff0c\u5f97\u5230\u7684\u539f\u59cb\u77e9\u9635\u53ef\u4ee5\u4f7f\u7528DESeq2\u5305\u5206\u6790\uff0c\u7b5b\u9009\u51fa\u5171\u6709\u7279\u6709\u6216\u8005\u5dee\u5f02\u7684peaks\u7b49\u8fdb\u884cpeaks\u7684\u6ce8\u91ca\u3002<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/655"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=655"}],"version-history":[{"count":2,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/655\/revisions"}],"predecessor-version":[{"id":657,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/655\/revisions\/657"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=655"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=655"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=655"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}