In this blog post, I\u2019ll give an overview of ways to share Genome Browser data views with others.<\/p>\n
Visualizing and sharing custom data is one of the most useful features of the UCSC Genome Browser tool. An independent review evaluating various genome browsers (http:\/\/tinyurl.com\/genome-browsers<\/a>), emphasized \u201cthe local and global exports for sharing sessions\u201d is one of the site\u2019s most \u201cattractive functionalities,\u201d with the report concluding that the UCSC Genome Browser \u201cis the best tool of our evaluation from that point of view.\u201d<\/p>\n Many veteran users are not aware of how easy it is to create and share browser views called sessions, especially using the more recent Public Sessions feature. Few users know that there are ways to modify URLs to share custom data, even to build URL links on top of data or sessions created by others. This blog post will give a wide overview of the many ways to share data on the Browser.<\/p>\n To access Sessions, under the top \u201cMy Data\u201d menu there is a \u201cMy Sessions\u201d option that leads to the page to create a URL snapshot of the view you are looking at in the Genome Browser. Once a user has created an account, on the Sessions Management page, they can then save a snapshot by giving the current view any \u201csessionName\u201d.\u00a0 A link, built from the userName and given sessionName, will be created that can be shared with others: https:\/\/genome.ucsc.edu\/<\/b>s\/userName\/sessionName<\/b><\/p>\n Once a session is created users have the option to click a \u201cdetails\u201d button on the Sessions Management page that leads them to an additional screen where they can enter a description. Newly created sessions are shareable by default, but can be made private (thereby requiring an account login to access), or they can be published to the Public Sessions page, where a search such as on the userName (https:\/\/genome.ucsc.edu\/cgi-bin\/hgPublicSessions?search=userName<\/b>) will bring up all sessions that the author published.<\/p>\n Public Sessions with descriptions are even more discoverable since matches will be returned on words found in the description. Public Sessions can be accessed under the \u201cMy Data\u201d menu and a search term can be entered in the box on the right, or a URL can be built to scan for specific search terms as illustrated above for userName. If you search \u201cprotein\u201d you will find all the sessions, for instance, that have mentioned protein in their description. Here\u2019s an example: http:\/\/genome.ucsc.edu\/cgi-bin\/hgPublicSessions?search=protein<\/a><\/p>\n Sometimes users want to hide all the tracks and only display certain data, and this can be done even without creating sessions. You can control the visibility of tracks from the URL with some of the following parameters<\/a>:<\/p>\n For example, you can use the following URL to hide every track (hideTracks=1), set the genome database to hg38 (db=hg38), set the mappability track to full visibility (mappability=full), and set the umap track height to 100 pixels (umap24Quantitative.heightPer=100): http:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?db=<\/strong>hg38&hideTracks=1<\/strong>&mappability=full<\/strong>&umap24Quantitative.heightPer=<\/strong>100 <\/a><\/p>\n Users can also share data with links without first creating a session by adding a \u201chgct_customText=\u201d parameter to their base URL. For instance, if a group has data for the human hg38 database in a web-accessible location that meets the criteria for loading as a custom track, they can build URL links in this fashion: https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?db=hg38&hgct_customText=http:\/\/location.online\/dataFile That online dataFile can be the track data, or a collection of more URLs to load more custom tracks. For instance, in a recent blog post about building bigBed tracks, https:\/\/bit.ly\/UCSC_blog_bigBed<\/a>, there was an example of hosting bigBed data at CyVerse. Since the data only displays in the position range of 1,405,000-1,448,000 on chromosome 5, a URL such as the below will load the hg19 genome (db=hg19) and go to a specific position (position=chr5:1405000-1448000) and then attach the remote file (hgct_customText=): https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?db<\/b>=hg19&position<\/b>=chr5:1405000-1448000&hgct_customText<\/b>=https:\/\/data.cyverse.org\/dav-anon\/iplant\/home\/brianlee\/Lab_Primers.bigBed<\/a><\/p>\n Once a user has taken the step to build binary-indexed files such as bigBeds or bigWigs, they can go a step further and put their collection of tracks into a Track Hub<\/a>. Track Hubs provide much more power for loading external data in more complex ways, such as enabling search indexes on uniquely named items in the remote data, or coloring tracks or individual elements.<\/p>\n Track Hubs are similar to the idea of having a text file that points to a collection of remotely hosted custom tracks. To make sharing easy, just one URL, called a hubUrl is given to the browser to load the Track Hub, and all the remotely hosted data, which must be in a binary-indexed format is then attached so only the data in the current view is transferred over the Internet. Here is a generic example of\u00a0 a link that would load hg38 track hub data: https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?db=hg38?hubUrl=http:\/\/location\/hub.txt<\/b><\/p>\n Here is a working example that loads onto the hg19 assembly (db=hg19) around a position (position=chr21:33,030,000-33,043,000) an example hub (hubUrl=): https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?db<\/b>=hg19&position<\/b>=chr21:33,030,000-33,043,000&hubUrl<\/b>=http:\/\/genome.ucsc.edu\/goldenPath\/help\/examples\/hubDirectory\/hub.txt<\/a><\/p>\n The UCSC Genome Browser provides a means to attach Track Hubs that can display novel genomes not hosted within the Browser. These are called assembly hubs.\u00a0 If a new assembly is being hosted remotely as an assembly hub, additional hub attachments also can be linked on top of that assembly hub, where the db= parameter is swapped with a genome= parameter as defined in the external assembly hub\u2019s genomes.txt file (or genomes stanza when useOneFile is applied \u2013see below).<\/p>\n In this following conceptual link, a genomeName is defined in an external assemblyHub.txt file that provides the Browser the underlying sequence of a declared genomeName. Then another collection of data, called hub.txt,\u00a0 is attached to that assembly hub, where that hub.txt is using the same genomeName in its genomes.txt file (or genome stanza). In the URL the very first parameter (genome=genomeName) tells the Browser that in one of these hubs there should be a similarly defined genome in order for the Browser to display the correct underlying sequence: https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?genome=genomeName&hubUrl=http:\/\/location\/assemblyHub.txt&hubUrl=http:\/\/location\/hub.txt<\/b><\/p>\n Just to illustrate how complex the system can get, a further step could also add custom tracks to the Assembly Hub, which has a Track Hub attached simultaneously: https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?genome=genomeName&hubUrl=http:\/\/location\/assemblyHub.txt&hubUrl=http:\/\/location\/hub.txt&hgct_customText=http:\/\/location.online\/dataFile<\/b><\/p>\n The new GenArk<\/a> assemblies come with quick links to load hubs from that collection. An example is https:\/\/genome.ucsc.edu\/h\/GCF_001984765.1<\/b><\/a>,<\/b> which will load the American beaver assembly (GCF_001984765.1). This short link is the equivalent of loading the hubUrl=https:\/\/hgdownload.soe.ucsc.edu\/hubs\/GCF\/001\/984\/765\/GCF_001984765.1\/hub.txt<\/a> and setting the genome=GCF_001984765.1 to the URL and pointing to the hgTracks CGI (the main Browser display).\u00a0 By condensing it all to this new short link format, we\u2019ve attempted to make loading GenArk hubs easier.<\/p>\n These https:\/\/genome.ucsc.edu\/h\/GCF_###<\/b> short links to GenArk assembly hubs can have additional parameters added to them, such as the following link that loads a custom track onto the GCF_001984765.1 assembly hub.\u00a0 The remote custom track in this example is a single bigBed hosted at CyVerse, where the URL is\u00a0 simultaneously setting the position to NW_017869957v1:1,437,578-1,648,889: https:\/\/genome.ucsc.edu\/h\/GCF_001984765.1?position<\/b>=NW_017869957v1:1,437,578-1,648,889&hgct_customText<\/b>=https:\/\/data.cyverse.org\/dav-anon\/iplant\/home\/brianlee\/examples\/GCF_001984765.1_C.can_genome_v1.0.cpgIslandExt.bb<\/a><\/p>\n A Track Hub can be attached to the Assembly Hub as seen in this version where the GCF_001984765.1assembly hub is redirected from the default position to NW_017869957v1:1,285,000-1,793,000 and the hubUrl= defines a CyVerse hosted hub.txt: https:\/\/genome.ucsc.edu\/h\/GCF_001984765.1?position=<\/b>NW_017869957v1:1,285,000-1,793,000&hubUrl<\/b>=https:\/\/data.cyverse.org\/dav-anon\/iplant\/home\/brianlee\/examples\/hub.txt<\/a><\/p>\n Track Hubs loaded on Assembly Hubs are not limited to GenArk hubs. The GenArk hubs have special privileges because they have short links. If you try to attach any hub with something like \u201cgenome GCF_###\u201d the Genome Browser will make an effort to find a match in the existing GenArk collection, and attach it automatically.<\/p>\n To illustrate how other assembly hubs outside of GenArk would work to have hubs attached, here is the longer version of the above link.\u00a0 In this case, the first hubUrl= is used to call out the location of this assembly hub, then the second hubUrl= is used again to load the second hub, and finally also hgct_customText comes into use to load a custom track<\/p>\n https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?hubUrl<\/b>=https:\/\/hgdownload.soe.ucsc.edu\/hubs\/GCF\/001\/984\/765\/GCF_001984765.1\/hub.txt&genome<\/b>=GCF_001984765.1&position<\/b>=NW_017869957v1:1,285,000-1,793,000&hubUrl<\/b>=https:\/\/data.cyverse.org\/dav-anon\/iplant\/home\/brianlee\/examples\/hub.txt&hgct_customText<\/b>=https:\/\/data.cyverse.org\/dav-anon\/iplant\/home\/brianlee\/examples\/GCF_001984765.1_C.can_genome_v1.0.cpgIslandExt.bb<\/a><\/p>\n<\/blockquote>\n The point of these rather tortuous examples is that multiple groups can own the sources of the data. Everything after the base URL, https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks<\/a>, can point to other places on the Internet with either the hubUrl= or hgct_customText= parameters. This means lab_X might have the assembly data, and lab_Y can generate a hub to view on that assembly, and lab_Z can further attach to those external groups even more custom data.\u00a0 And all this sharing and interoperability can happen without ever creating session links.<\/p>\n Using sessions is powerful since it lets you customize your view of the Genome Browser. Users can create a session (or borrow another from the Public Session page) and use that session\u2019s userName and sessionName to attach their own custom data.<\/p>\n This can have the advantage of creating shorter links or also preconfiguring the browser to a certain position or display.\u00a0 We recently added the ability to customize the font on the Browser so a session can even be used just as a different way of viewing the same data stylistically, for instance making the display easier for you to read.<\/p>\n Here are some real-world examples borrowing from real Public Sessions.\u00a0 To load on a Public Session, go to the \u201cMy Data\u201d menu, then choose \u201cPublic Sessions\u201d, and then you can click on the image of any session to load it. You can build your own URL from an existing Public Session by noting the Author field (equivalent to the session\u2019s source userName) and the Session Name field, like so: https:\/\/genome.ucsc.edu\/s\/userName\/sessionName<\/b><\/p>\n Here\u2019s a session on hg19 that will load and also attach the earlier CyVerse custom track: https:\/\/genome.ucsc.edu\/s\/brianlee\/AvantG_Font?position<\/b>=chr5:1405000-1448000&hgct_customText<\/b>=https:\/\/data.cyverse.org\/dav-anon\/iplant\/home\/brianlee\/Lab_Primers.bigBed<\/a><\/p>\n Here\u2019s one that will load a few hubs on a session that points to hg38 and also opens the display to\u00a0 the SIRT1 gene using the &singleSearch=knownCanonical&position=SIRT1 parameters: https:\/\/genome.ucsc.edu\/s\/brianlee\/Times_Font?hubUrl=<\/b>http:\/\/fantom.gsc.riken.jp\/5\/datahub\/hub.txt&hubUrl<\/b>=http:\/\/expdata.cmmt.ubc.ca\/JASPAR\/UCSC_tracks\/hub.txt&hubUrl<\/b>=http:\/\/remap.univ-amu.fr\/storage\/public\/hubReMap2020UCSC\/hub.txt&singleSearch=knownCanonical&position=<\/b>SIRT1<\/a><\/p>\n Again, these complex links are to illustrate that there are multiple ways to view multiple groups of data across the world in the Genome Browser. You can get to the data either through clicks and searches on the website or by building Sessions or Public Sessions and URL links to remotely hosted data.\u00a0 This blog post could not cover every topic but gives a good introduction to the ways to share data with sessions or complex URLs. To learn more about links, see these documentation pages:<\/p>\n Links to guides for Sessions, Track Hubs, Custom Tracks, and videos can be found on our training page:<\/p>\n This entry written by Brian Lee. If after reading this blog post you have any questions, please email genome@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genome-www@soe.ucsc.edu.<\/p>\n\n\n In this blog post, I\u2019ll give an overview of ways to share Genome Browser data views with others. Visualizing and sharing custom data is one of the most useful features of the UCSC Genome Browser tool. An independent review evaluating various genome browsers (http:\/\/tinyurl.com\/genome-browsers), emphasized \u201cthe local and global exports for sharing sessions\u201d is one […]<\/p>\n","protected":false},"author":13,"featured_media":1080,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-883","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-uncategorized"],"jetpack_featured_media_url":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-content\/uploads\/2021\/08\/URL_share.png","_links":{"self":[{"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/posts\/883","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/comments?post=883"}],"version-history":[{"count":25,"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/posts\/883\/revisions"}],"predecessor-version":[{"id":1081,"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/posts\/883\/revisions\/1081"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/media\/1080"}],"wp:attachment":[{"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/media?parent=883"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/categories?post=883"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/genome-blog.gi.ucsc.edu\/blog\/wp-json\/wp\/v2\/tags?post=883"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}\n
SESSIONS AND PUBLIC SESSIONS<\/b><\/h2>\n
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BUILDING URLS TO SET TRACK VISIBILITIES
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BUILDING URLS TO CUSTOM TRACKS<\/b><\/h2>\n
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BUILDING URLS TO TRACK HUBS<\/b><\/h2>\n
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BUILDING URLS TO TRACK HUBS ON ASSEMBLY HUBS<\/b><\/h2>\n
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ASSEMBLY HUB EXAMPLES WITH GenArk HUBS<\/b><\/h2>\n
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genome GCF_001984765.1<\/code>” for the genomes stanza (since it is using useOneFile on and is also expecting to find a GenArk hub).\u00a0 It relies entirely on the GenArk assembly hub for the underlying assembly information.<\/li>\n<\/ul>\n\n
BUILDING URLS ATTACHING TRACK HUBS AND CUSTOM TRACKS TO SESSIONS<\/b><\/h2>\n
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<\/b><\/li>\n<\/ul>\n\n
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