{"id":332,"date":"2018-12-16T14:50:00","date_gmt":"2018-12-16T06:50:00","guid":{"rendered":"https:\/\/www.next-bioinfo.tw\/?p=332"},"modified":"2023-09-27T14:57:36","modified_gmt":"2023-09-27T06:57:36","slug":"%e3%80%903d-genome%e3%80%91-%e6%9f%93%e8%89%b2%e8%b3%aa%e7%92%b0loop%e7%9a%84bedpe%e6%a0%bc%e5%bc%8f","status":"publish","type":"post","link":"https:\/\/www.next-bioinfo.tw\/en\/2018\/12\/%e3%80%903d-genome%e3%80%91-%e6%9f%93%e8%89%b2%e8%b3%aa%e7%92%b0loop%e7%9a%84bedpe%e6%a0%bc%e5%bc%8f\/","title":{"rendered":"\u30103D Genome\u3011 BEDPE the format of chromatin looping"},"content":{"rendered":"

BEDPE (.bedpe) was a format extended from BED format for 2 dimension information. Because the BED format was designed for 1 dimension feature such as ChIP-Seq data which could not represent two loci for a single data point, BEDPE was introduced and was supported by massive data analysis tools in recent days and has become a standard. Especially in representing chromosome looping the common format is BEDPE8 and BEDPE10. When we used hichipper to analyze HiChIP data, the output of loops was stored in BEDPE8 format.<\/p>\n\n\n\n

For example:<\/p>\n\n\n\n

<\/path><\/path><\/svg><\/span>
chr1<\/span>  <\/span>10<\/span>   <\/span>20<\/span>   <\/span>chr5<\/span>  <\/span>50<\/span>  <\/span>51<\/span>  <\/span>.<\/span>  <\/span>2<\/span><\/span><\/code><\/pre><\/div>\n\n\n\n
The fields in order are:<\/p>\n\n\n\n
<\/path><\/path><\/svg><\/span>
chr_A<\/span> <\/span>\/<\/span> <\/span>start_A<\/span> <\/span>\/<\/span> <\/span>end_A<\/span> <\/span>\/<\/span> <\/span>chr_B<\/span> <\/span>\/<\/span> <\/span>start_B<\/span> <\/span>\/<\/span> <\/span>end_B<\/span> <\/span>\/<\/span> <\/span>record_name<\/span> <\/span>\/<\/span> <\/span>score<\/span> <\/span>\/<\/span> <\/span>strand_A<\/span> <\/span>\/<\/span> <\/span>strand_B<\/span><\/span><\/code><\/pre><\/div>\n\n\n\n
    \n
  1. A's chromosome number<\/li>\n\n\n\n
  2. A's start position<\/li>\n\n\n\n
  3. A's end position<\/li>\n\n\n\n
  4. B's chromosome number<\/li>\n\n\n\n
  5. B's start position<\/li>\n\n\n\n
  6. B's end position<\/li>\n\n\n\n
  7. The name of this data point (if Null can fill with a dot \".\" )<\/li>\n\n\n\n
  8. Intensity of this data point.<\/li>\n\n\n\n
  9. A`strand(transcription direction)<\/li>\n\n\n\n
  10. B`strand(transcription direction)<\/li>\n<\/ol>\n\n\n\n
    For the chromatin loop (looping), A and B are the two anchor points of the loop (loop anchors). Those two positions are also where the chromatin loop starts and ends.<\/p>\n\n\n\n
    References:<\/p>\n\n\n\n
    https:\/\/bedtools.readthedocs.io\/en\/latest\/content\/general-usage.html
    https:\/\/github.com\/YaqiangCao\/cLoops\/blob\/master\/scripts\/hicpropairs2bedpe<\/p>","protected":false},"excerpt":{"rendered":"
    BEDPE(.bedpe)\u70baBED\u683c\u5f0f\u7684\u4e8c\u7dad\u64f4\u5145\u3002\u7531\u65bcBED\u683c\u5f0f\u8a2d\u8a08\u6210\u7d00\u9304\u4e00\u7dad\u7684\u7279\u5fb5\u8cc7\u8a0a(\u4f8b\u5982ChIP Seq […]<\/p>","protected":false},"author":1,"featured_media":333,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_mi_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"site-container-style":"default","site-container-layout":"default","site-sidebar-layout":"default","site-transparent-header":"default","disable-article-header":"default","disable-site-header":"default","disable-site-footer":"default","disable-content-area-spacing":"default","footnotes":""},"categories":[20],"tags":[39,38,27,37],"_links":{"self":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/332"}],"collection":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/comments?post=332"}],"version-history":[{"count":1,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/332\/revisions"}],"predecessor-version":[{"id":334,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/332\/revisions\/334"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media\/333"}],"wp:attachment":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media?parent=332"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/categories?post=332"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/tags?post=332"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}