90c7c79830fcf633543d0fdb16fdbc21f1ae6e6f max Fri Apr 21 02:42:26 2023 -0700 #Preview2 week - bugs introduced now will need a build patch to fix various doc fixes related to bigDataIndex, no redmine, email and galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3 diff --git src/hg/htdocs/goldenPath/help/cram.html src/hg/htdocs/goldenPath/help/cram.html index 29d1865..b3de4c3 100755 --- src/hg/htdocs/goldenPath/help/cram.html +++ src/hg/htdocs/goldenPath/help/cram.html @@ -33,31 +33,32 @@ The track lines to describe CRAM tracks are identical to track lines for BAM tracks. This includes the <code>type</code> parameter, which is still <code>bam</code> even for CRAM tracks. The only difference is that instead of providing the URL to a BAM file, the URL instead points to a CRAM file.</p> <p> Please also note that just as a BAM file requires an associated BAM.bai index file, a CRAM file will require an associated CRAM.crai index file in the same location to load.</p> <h2>Example #1</h2> <p> Here is an example CRAM track that displays around the gene SOD1 on hg19 that can be cut and pasted as text into the <a href="/cgi-bin/hgCustom?db=hg19" target="_blank">Custom Tracks</a> page:</p> <pre><code>track type=bam db=hg19 name=exampleCRAM bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram </code></pre> <p> Please note at the above URL location there is also a -<code>http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram.crai</code> file.</p> +<code>http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram.crai</code> file. If this .crai file is at a different URL, +the <code>bigDataIndex=<URL></code> option must be added.</p> <p> Clicking this following link will also load the above track. The information following <code>hgct_customText</code> is equivalent to pasting the text in to the Custom Tracks page:</p> <pre><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570&hgct_customText=track%20type=bam%20name=exampleCRAM%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram" target="_blank"><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570&<strong>hgct_customText=</strong>track%20type=bam%20name=exampleCRAM%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram</code></a></pre> <h2>Example #2</h2> <p> If the URL to a CRAM file ends with .cram, you can paste the URL directly into the custom track management page, click submit and view it in the Browser. The track name will then be the name of the file. If you want to configure the track name and descriptions, you will need to create a track line, as shown in the above example. Learn more about track line options and configuring custom tracks <a href="hgTracksHelp.html#TRACK" target="_blank">here</a>.</p> <p> Here is an example URL to a CRAM file from the 1000 Genomes Project that can be pasted directly into