{"action":"created","issue":{"url":"https://api.github.com/repos/WormBase/website/issues/6296","repository_url":"https://api.github.com/repos/WormBase/website","labels_url":"https://api.github.com/repos/WormBase/website/issues/6296/labels{/name}","comments_url":"https://api.github.com/repos/WormBase/website/issues/6296/comments","events_url":"https://api.github.com/repos/WormBase/website/issues/6296/events","html_url":"https://github.com/WormBase/website/issues/6296","id":309514224,"number":6296,"title":"Request: Display splice junction prevalence on gene page and/or JBrowse","user":{"login":"chris-grove","id":611382,"avatar_url":"https://avatars1.githubusercontent.com/u/611382?v=4","gravatar_id":"","url":"https://api.github.com/users/chris-grove","html_url":"https://github.com/chris-grove","followers_url":"https://api.github.com/users/chris-grove/followers","following_url":"https://api.github.com/users/chris-grove/following{/other_user}","gists_url":"https://api.github.com/users/chris-grove/gists{/gist_id}","starred_url":"https://api.github.com/users/chris-grove/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chris-grove/subscriptions","organizations_url":"https://api.github.com/users/chris-grove/orgs","repos_url":"https://api.github.com/users/chris-grove/repos","events_url":"https://api.github.com/users/chris-grove/events{/privacy}","received_events_url":"https://api.github.com/users/chris-grove/received_events","type":"User","site_admin":false},"labels":[{"id":16588072,"url":"https://api.github.com/repos/WormBase/website/labels/Webteam","name":"Webteam","color":"a369e7","default":false},{"id":2288092,"url":"https://api.github.com/repos/WormBase/website/labels/feature%20request","name":"feature request","color":"02d7e1","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":17,"created_at":"2018-03-28T20:12:38Z","updated_at":"2018-05-02T14:40:43Z","closed_at":null,"author_association":"MEMBER","body":"At the 2017 International C. elegans Meeting, there was a presentation by Denis Dupuy in which his lab had developed software to calculate (using RNAseq data) and display the prevalence of various splice junctions for genes with different splice variants/isoforms. The point of this type of display is to present to users which splice variants are actually abundant or have a significant presence in vivo in contrast to splice variants that are only present in a small fraction of the reads. The paper from the Dupuy lab came out in December:\r\n\r\nhttps://www.ncbi.nlm.nih.gov/pubmed/29089372\r\n\r\nThis set off an email thread between Denis, @gw3 @khowe @scottcain and myself.\r\n\r\nThere was discussion about other potential technologies to achieve the same goal, such as LeafCutter:\r\n\r\nPaper:\r\nhttps://www.ncbi.nlm.nih.gov/pubmed/29229983\r\n\r\nSite:\r\nhttps://davidaknowles.github.io/leafcutter/\r\n\r\nI'm creating this ticket to keep track of the conversation and any ideas on implementation that we might come up with. I think this is an important feature, particularly for complex loci with 10+ isoforms:\r\n\r\nhttp://www.wormbase.org/species/c_elegans/gene/WBGene00006759#09g--10\r\nhttp://www.wormbase.org/species/c_elegans/gene/WBGene00006767#09g--10\r\nhttp://www.wormbase.org/species/c_elegans/gene/WBGene00003150#09g--10\r\n\r\nOf course, whatever technology we go with we would want it to be able to be run automatically during the build with updated RNA-seq data.\r\n"},"comment":{"url":"https://api.github.com/repos/WormBase/website/issues/comments/386001281","html_url":"https://github.com/WormBase/website/issues/6296#issuecomment-386001281","issue_url":"https://api.github.com/repos/WormBase/website/issues/6296","id":386001281,"user":{"login":"scottcain","id":274751,"avatar_url":"https://avatars0.githubusercontent.com/u/274751?v=4","gravatar_id":"","url":"https://api.github.com/users/scottcain","html_url":"https://github.com/scottcain","followers_url":"https://api.github.com/users/scottcain/followers","following_url":"https://api.github.com/users/scottcain/following{/other_user}","gists_url":"https://api.github.com/users/scottcain/gists{/gist_id}","starred_url":"https://api.github.com/users/scottcain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/scottcain/subscriptions","organizations_url":"https://api.github.com/users/scottcain/orgs","repos_url":"https://api.github.com/users/scottcain/repos","events_url":"https://api.github.com/users/scottcain/events{/privacy}","received_events_url":"https://api.github.com/users/scottcain/received_events","type":"User","site_admin":false},"created_at":"2018-05-02T14:40:43Z","updated_at":"2018-05-02T14:40:43Z","author_association":"CONTRIBUTOR","body":"@chris-grove and @gw3  JBrowse can't really do on the fly normalization like that; it would require some precomputing.  I can imagine writing a script to do that analysis (read in gene gff, saving boundaries; read in introns, counting those that fall within boundaries; looping through each gene and calculating a normalized read count; spit out gff).  If such a thing existed, would it have to be redone with each release, or do these intron data get added to on regular (or irregular) basis?"}}
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