ce5eff33ee510ad5dd99477ba0b11e2d9168505e brianlee Sat May 14 06:59:36 2022 -0700 Updating other doc references to resetting browser diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index a219f60..386e581 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -928,52 +928,52 @@ <strong><em>Problem:</em></strong> When I click the <em>submit</em> button, I get the error message "line # of custom input: BED chromStarts[i] must be in ascending order".<br> <strong><em>Solution:</em></strong> This is most likely caused by a logical conflict in the Genome Browse software. It accepts custom GFF tracks that have multiple "exons" at the same position, but not BED tracks. Because the browser translates GFF tracks to BED format before storing the custom track data, GFF tracks with multiple exons will case an error when the BED is read back in. To work around this problem, remove duplicate lines in the GFF track.</p> <p> <strong><em>Problem:</em></strong> When I click the <em>submit</em> button, the Genome Browser track window displays OK, but my track isn't visible.<br> <strong><em>Solution:</em></strong> Check the browser and track lines in your annotation file to make sure that you haven't accidentally set the display mode for the track to <em>hide</em>. If you are using the Annotation File box on the Genome Browser Gateway page to upload the track, check that you've entered the correct file name. If neither of these is the cause of the problem, try resetting the Genome Browser to clear any settings that may be preventing the annotation to display. To reset -the Genome Browser, click the <em>Click here to reset</em> link on the Gateway page. If the +the Browser, click the "Reset All User Settings" under the top blue Genome Browser menu. If the annotation track still doesn't display, you may need to clear the cookies in your Internet browser as well (refer to your Internet browser's documentation for further information).</p> <p> <strong><em>Problem:</em></strong> I am trying to upload some custom tracks (.gz files) to the Genome Browser using a URL from a GEO query. However, the upload is failing with the error "line 1 of <filename>.gz: thickStart after thickEnd".<br> <strong><em>Solution:</em></strong> The custom track mechanism supports plain BED files (not bigBed) that are of the type <a href="../../FAQ/FAQformat.html#format13">broadPeak</a> or <a href="../../FAQ/FAQformat.html#format12">narrowPeak</a>. Set the track attribute <a href="#TRACK">type=<<em>track_type</em>></a> to enable the loader to correctly process the special columns at the end of each line. Your track type entry should consist of two lines: the first to define the track type and the second to specify the URL. For example:</p> <pre><code>track type=<font color="000099">broadPeak</font> https://www.ncbi.nlm.nih.gov/geosuppl/...</code></pre> <p> <strong><em>Problem:</em></strong> I've gotten my annotation track to display, but now I can't make it go away! How do I remove an annotation track from my Genome Browser display?<br> <strong><em>Solution:</em></strong> To remove only one track, click the <em>Manage Custom Tracks</em> button and delete the desired track using the checkbox and Delete button. To quickly -remove all of your custom tracks, reset the Genome Browser to its default settings by clicking the -<em>Click here to reset</em> link on the Gateway page. Note that this reset will also remove any +remove all of your custom tracks, reset the Genome Browser to its default settings by clicking on +"Reset All User Settings" under the top blue Genome Browser menu. This reset will also remove any other customizations you have made to your Genome Browser display.</p> <p> <strong><em>Problem:</em></strong> I put my custom track files on Dropbox, Apple iCloud, Google Drive, Amazon Drive, Box.com, Microsoft OneDrive, or another "online cloud backup" provider and they will not display in the browser. Why? <br> <em>OR</em><br> <strong><em>Problem:</em></strong> When I try to visualize my custom tracks in the Browser, I receive the error message "Byte-range request was ignored by server".<br> <strong><em>Solution:</em></strong> Backup providers used to work for hosting simple text-based custom tracks, but things have changed. For large custom track data sets, the use of indexed binary formats such as bigBed and bigWig is preferable and usually fail with backup providers. These formats provide much faster display performance because only the portion of the file needed to display the currently viewed region must be