type parameter, which is still bam 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.
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.
Here is an example CRAM track that displays around the gene SOD1 on hg19 that can be cut and pasted as text into the Custom Tracks page:
track type=bam db=hg19 name=exampleCRAM bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram
Please note at the above URL location there is also a
-http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram.crai file.
http://genome.ucsc.edu/goldenPath/help/examples/cramExample.cram.crai file. If this .crai file is at a different URL,
+the bigDataIndex=<URL> option must be added.
Clicking this following link will also load the above track. The information following
hgct_customText is equivalent to pasting the text in to the Custom Tracks page:
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.cramIf 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 here.
Here is an example URL to a CRAM file from the 1000 Genomes Project that can be pasted directly into