{"id":1034,"date":"2007-06-07T12:19:00","date_gmt":"2007-06-07T11:19:00","guid":{"rendered":"http:\/\/www.wjst.de\/blog\/2007\/06\/07\/genome-browser-bug\/"},"modified":"2007-06-07T13:24:33","modified_gmt":"2007-06-07T12:24:33","slug":"genome-browser-bug","status":"publish","type":"post","link":"https:\/\/www.wjst.de\/blog\/sciencesurf\/2007\/06\/genome-browser-bug\/","title":{"rendered":"Genome Browser Bug"},"content":{"rendered":"<p>Here I describe a bug in the UCSC Genome Browser display that I found this morning. When locating a SNP on the human genome (where I have only surrounding sequence) I usually do a quick BLAT search<!--more--> of my sequence with the SNP base being deleted. This will show up as 1 bp gap that can be easily matched to exon-intron structure or reading frame. Occasionally, however, there is a +1 bp offset of my artifical gapwhich would let me draw wrong conclusions. My BLAT search below has the name &#8220;rs2067694&#8221; and shoudl match the SNP indicated in the bottom line.<\/p>\n<p><a href=\"https:\/\/www.wjst.de\/blog\/wp-content\/uploads\/2007\/06\/ucsc_bug2.png\" title='' data-rel=\"key-image-0\" data-rl_title=\"\" data-rl_caption=\"\"><img src='https:\/\/www.wjst.de\/blog\/wp-content\/uploads\/2007\/06\/ucsc_bug2.png' alt='ucsc_bug2.png' \/><\/a><\/p>\n<p>If you want to use my settings, cut &#038; paste &#8220;http:\/\/www.wjst.de\/wjst_snp.ini&#8221; into <a href=\"http:\/\/genome.ucsc.edu\/cgi-bin\/hgSession?org=Human&#038;db=hg17&#038;hgsid=93605511&#038;hgS_doMainPage=1\">this linked page<\/a>.<\/p>\n\n<p>&nbsp;<\/p>\n<div class=\"bottom-note\">\n  <span class=\"mod1\">CC-BY-NC Science Surf , accessed 07.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"<p>Here I describe a bug in the UCSC Genome Browser display that I found this morning. When locating a SNP on the human genome (where I have only surrounding sequence) I usually do a quick BLAT search &nbsp; CC-BY-NC Science Surf , accessed 07.04.2026<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2,9],"tags":[1100,1099,962,1098],"class_list":["post-1034","post","type-post","status-publish","format-standard","hentry","category-genetics-biology","category-computer-software","tag-bug-report","tag-genome_browser","tag-human_genome","tag-reading_frame"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1034","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=1034"}],"version-history":[{"count":0,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1034\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=1034"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=1034"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=1034"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}