table bigGenePred
"bigGenePred gene models"
(
string chrom; "Reference sequence chromosome or scaffold"
uint chromStart; "Start position in chromosome"
@@ -240,30 +239,67 @@
To view this example, you can click this into this Browser link. To view your own data, paste the
link into your web browser and replace the URL after "bigDataUrl=" with a link to your own
hosted data.
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr19:44905790-44909388&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredEx4.bb
You can also add your data in the custom track management
page. This allows you to set position, configuration options, and write a more complete
desciption. If you want to see codons, you can right click, then click configure codon view or
set this options using baseColorDefault=genomicCodons as is done below.
browser position chr19:44905790-44909388
track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Four" description="Ex4:BigGenePred Made from GTF" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredEx4.bb
Once you are done, you should have a track on the Genome Browser like the one below.
+
+Example #5: Create a BigGenePred Track Hub
+In this example, you will set up a Track Hub that displays bigGenePred data and uses one of the
+bigGenePred-specific settings to display gene codons. For more instruction on bigGenePred track
+hubs, please visit the
+bigGenePred example description page. For complete instructions on Track Hubs, visit
+the Track Hub set-up page.
+
+- Make sure you have access to a web-hosted file location like GitHub, CyVerse, or an
+institutional website. This is where you will store your bigData files and configuration files.
+For more information, please visit the hosting section of
+our Track Hub help guide.
+- Copy the text from the bigGenePred example hub files
+into files on your hosting website. You will need a hub.txt and a genomes.txt file, along with
+a directory for each assembly you would like to display data on (e.g., hg38). Within your assembly
+directory, you will need your data file(s), (e.g., bigGenePredEHub.bb). Then you will need a
+trackDb.txt file which will define your track settings, such as the setting that displays
+genomic codons and amino acid letters,
baseColorDefault genomicCodons.
+- Verify that you have the four required files in the following structure, where hg38 is a directory:
+
+--hub.txt
+--genomes.txt
+--hg38
+----trackDb.txt
+----bigGenePred.bb
+
+- Copy the link to your hub.txt file URL of your hub.txt file and paste it into the text input
+box on the Track Hub page. For an example, you can paste
+the following link into the input box:
+
+http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubBigGenePred/hub.txt.
+This should connect you to your hub, with the data available by navagating to your
+assembly of interest.
+
+ 
+
+
Sharing your data with others
If you would like to share your bigGenePred data track with a colleague, learn how to create a URL
link to your data by looking at Example #6 on the
custom track help page.
Extracting data from bigBed format
Because the bigGenePred files are an extension of bigBed files, which are indexed binary files, it
can be difficult to extract data from them. UCSC has developed the following programs to
assist in working with bigBed formats, available from the
binary utilities directory.
-
bigBedToBed — converts a bigBed file to ASCII BED format.