Since CRAM files are more dense than BAM files, many groups
are switching to the CRAM format to save disk space. For CRAM tracks to load there is an expectation
that the checksum of the reference sequence used to create the CRAM will be in the CRAM header. A
file with a matching checksum is also expected to be accessible from the EBI RefGet CRAM reference registry
(see References for CRAM resources). Otherwise, users must specify a
refUrl setting that will point to a server that is offering up the reference sequences
(see Example Four).
Since the loading of CRAM data requires the specific reference sequence used to create the CRAM
file, it is very important that the exact same reference sequence is used for compression and
decompression. When a CRAM file is first loaded on a given chromosome, a check for the preexistence
in a special browser "cramCache" directory of the specified reference checksum will take
place. If the reference sequence information specific for that CRAM for the currently viewed
chromosome region does not exist, a message will display about the file not being found along with
-a note about downloading the reference from the EBI CRAM reference registry if it is available (or
-from another Refget server using refUrl). A refresh of the page once the download is complete will
-display the CRAM data as if it were a BAM file.
refUrl setting. A refresh of the page once the download is
+complete will display the CRAM data as if it were a BAM file.
The track lines to describe CRAM tracks are identical to track lines for BAM tracks. This includes
the 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
@@ -84,37 +84,36 @@
User Guide and associated Quick Start Guides to
building hubs. Note that type bam is used to display CRAM files in hubs, just as
type bam is used in custom CRAM tracks.
track cram61
type bam
shortLabel HG00361
longLabel This CRAM file is from the 1000 Genomes Project HG00361
visibility pack
bigDataUrl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00361/exome_alignment/HG00361.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.cram
For genomes that are not registered in the EBI CRAM Reference Registry,
the refUrl setting is used to point the browser to
-the appropriate place to find the reference sequence. The refUrl
-takes an argument of the URL of the reference server with a %s being
-replaced the RefGet MD5 checksum that identifies the reference sequence.
+the appropriate place to find the reference sequence. The refUrl setting is used with
+the URL of the reference server, such as refUrl http://university.edu/URL/cramRef/%s
+where the %s gets replaced by the RefGet MD5 checksum which identifies the reference
+sequence.
-
-The below example is a hub track stanza using therefUrl
-option:
+The example below shows a hub track stanza using the refUrl setting:
track cramExample
type bam
visibility full
shortLabel cramExRefUrl
longLabel This CRAM file points to a reference sequence specified by refUrl
refUrl http://university.edu/URL/cramRef/%s
bigDataUrl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
The use of refUrl can also be employed on a custom track line:
track type=bam db=hg19 name=cramExRefUrl
refUrl=http://university.edu/URL/cramRef/%s
bigDataUrl=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram