c0a631c93bb41116a873c46ee13c87c5d0806c46 lrnassar Fri Mar 24 16:18:39 2023 -0700 Adding new FAQ entry for diagnosing slow hgTracks behavior. Refs #30620 diff --git src/hg/htdocs/FAQ/FAQtracks.html src/hg/htdocs/FAQ/FAQtracks.html index 267fb62..31988d8 100755 --- src/hg/htdocs/FAQ/FAQtracks.html +++ src/hg/htdocs/FAQ/FAQtracks.html @@ -1,52 +1,133 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Genome Browser Tracks</h1> <h2>Topics</h2> <ul> +<li><a href="#speed">Why is my tracks display slow?</a></li> <li><a href="#tracks0">List of tracks available for a specific assembly</a></li> <li><a href="#tracks1">Database/browser start coordinates differ by 1 base</a></li> <li><a href="#tracks2">mRNA-associated results</a></li> <li><a href="#tracks3">Correspondence of Genome Browser mRNA positions to those of OMIM genes</a></li> <li><a href="#tracks4">Position changes of features</a></li> <li><a href="#tracks6">Evaluating possible alternative splices</a></li> <li><a href="#tracks7">Matching exons and protein sequence</a></li> <li><a href="#tracks9">Cause of duplicated gene</a></li> <li><a href="#tracks11">Protein doesn't begin with methionine</a></li> <li><a href="#tracks12">Doing an orthology track analysis of a protein</a></li> <li><a href="#tracks14">Quality benchmarks for predicted genes</a></li> <li><a href="#tracks15">Display conventions for gene prediction tracks</a></li> <li><a href="#tracks16">Viewing detailed displays in conservation tracks</a></li> <li><a href="#tracks17">Negative strand coordinates in PSL files</a></li> <li><a href="#tracks18">Inconsistency in stop codon treatment in GTF tracks</a></li> <li><a href="#tracks19">Obtaining clones referenced in Genome Browser</a></li> <li><a href="#tracks20">Locating centromeres and telomeres</a></li> <li><a href="#tracks21">Determining the table name for an annotation track</a></li> <li><a href="#tracks22">Unexpected results in UCSC RefSeq track</a></li> </ul> <hr> <p> <a href="index.html">Return to FAQ Table of Contents</a></p> +<a name="speed"></a> +<h2>Why is my tracks display slow?</h2> +<p> +There are different reasons why the Genome Browser tracks display can become slow. +Below is a list of common scenarios alongside potential solutions. The most common +reason involves the configuration settings that are saved as users interact with +the Genome Browser, such as track visibilities and custom data. +This can be solved by a reset of all your current Genome Browser session +information although it is important to note that this will reset all +settings including filters, track order and remove all custom data. To do +this, click "Genome Browser" > "Reset +All User Settings" in the top blue bar menu or +<a href="../cgi-bin/cartReset" onclick="return confirm('Warning: Reseting all settings '+ +'will return the Genome Browser to a fresh browsing session. All settings including '+ +'filters, visibilities, and custom data will be lost.')">click here</a>.</p> +<p> +If none of the scenarios below improve +the browsing speed, you may also save a <a href="../cgi-bin/hgSession" +target="_blank">session</a> of a display that is slow to load and send it +to us as genome-www@soe.ucsc.edu so that we may provide further guidance.</p> + +<h6>Problem: Too many tracks on at once, or the viewing window is too large.</h6> +<p> +Drawing the tracks image can become a cumbersome task when too many tracks are +enabled and/or if the viewing window is too large. Setting some track visibilities +to <b>hide</b> or zooming into a smaller window should alleviate this problem. +Another consideration is to reduce the visibilities of tracks by by setting them to +<b>dense</b> visibilitiy instead of full/pack/squish. +That will also speed up the drawing.</p> + +<h6>Problem: Large amount of <a href="../cgi-bin/hgCustom">custom tracks</a>.</h6> +<p> +Having a large number of custom tracks loaded can lead to a slowdown. However, the slowdown +should be minimal unless a large number of tracks are turned on. +Custom tracks can be hidden like any other track, or they can also be entirely removed +from the <a href="../cgi-bin/hgCustom">custom tracks</a> page.</p> +<p> +It is also possible to completely reset the Genome Browser +session, which will remove all settings including filters, track order, +and all custom data. To do this, click "Genome Browser" > "Reset +All User Settings" in the top blue bar menu or +<a href="../cgi-bin/cartReset" onclick="return confirm('Warning: Reseting all settings '+ +'will return the Genome Browser to a fresh browsing session. All settings including '+ +'filters, visibilities, and custom data will be lost.')">click here</a>.</p> + +<h6>Problem: Large amount of big data/remote files, such as +<a href="../cgi-bin/hgHubConnect" target="_blank">hubs</a>.</h6> +<p> +Like custom tracks, this slowdown should only be a problem if a large number of tracks +are turned on. However, with remote data there are other considerations that may speed +up performance. When retrieving remote files, consider that you are sending a request +to UCSC, which is then asking for the data wherever it is hosted. So the data must regularly +travel between the hosting location and the Genome Browser servers in CA (main site), Germany +(European mirror), or Japan (Asian mirror). If the hosting connection is unstable, or the +distance between any of +these steps is great, it can lead to slow data display. Consider that many of our free +<a href="../goldenPath/help/hgTrackHubHelp#Hosting" target="_blank">hosting options</a> can +inherently be slow as they are designed for accessibility and not speed. Likewise if you +are using google/amazon storage consider the performance that was purchased as it could +be a playing factor.</p> +<p> +While improving the connection of the hosting location may help, there are other solutions +which do not require the file to be moved. UCSC hosts mirrors in Europe +(https://genome-euro.ucsc.edu/) as well as Asia (https://genome-asia.ucsc.edu/) which should +be faster. In some +extreme circumstances a local installation of the Genome Browser may suit your needs. This +would allow you to load all the custom annotations locally without having to traverse over +the web. In order to learn more about this option see our +<a href="../goldenPath/help/mirror.html" target="_blank">mirroring page</a>.</p> + +<h6>Problem: Slow or unreliable internet connection.</h6> +<p> +If your connection is slow or unreliable, you may want to consider our mirror sites closer to +your location. +UCSC hosts mirrors in Europe (https://genome-euro.ucsc.edu/) as well as Asia +(https://genome-asia.ucsc.edu/) which should be faster. +In some extreme circumstances a local installation of the Genome Browser may +suit your needs. In order to learn more about this option see our +<a href="../goldenPath/help/mirror.html" target="_blank">mirroring page</a>.</p> + <a name="tracks0"></a> <h2>List of tracks available for a specific assembly</h2> <h6>How can I find out which tracks have been released for the assembly in which I'm interested?</h6> <p> The <a href="/goldenPath/releaseLog.html" target="_blank">Release Log</a> contains lists of the published tracks and release dates for the current set of genome assemblies available on our site. It also shows version information for the assemblies of other species used in comparative genomics tracks.</p> <a name="tracks1"></a> <h2>Database/browser start coordinates differ by 1 base</h2> <h6>I am confused about the start coordinates for items in the refGene table. It looks like you need to add "1" to the starting point in order to get the same start coordinate as is shown by the Genome Browser. Why is this the case?</h6>