Step 2. If you would like to include optional reading frame and block summary information, download the chr22_KI270731v1_random.gp genePred file.
Step 3.
Download the autoSql file bigMaf.as needed by
bedToBigBed. If you have opted to include the optional frame summary and information
with your bigMaf file, you must also download the autoSql files
mafSummary.as and
mafFrames.as files.
+Here are wget commands to obtain the above files and the hg38.chrom.sizes file mentioned below: +
wget https://genome.ucsc.edu/goldenPath/help/examples/chr22_KI270731v1_random.maf
+wget https://genome.ucsc.edu/goldenPath/help/examples/chr22_KI270731v1_random.gp
+wget https://genome.ucsc.edu/goldenPath/help/examples/bigMaf.as
+wget https://genome.ucsc.edu/goldenPath/help/examples/mafSummary.as
+wget https://genome.ucsc.edu/goldenPath/help/examples/mafFrames.as
+wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
+
Step 4.
Download the bedToBigBed and mafToBigMaf programs from the UCSC
binary utilities directory. If you have
opted to generate the optional frame and summary files for your multiple alignment, you must also
download the hgLoadMafSummary, genePredSingleCover, and
genePredToMafFrames programs from the same
directory.
Step 5.
Use the fetchChromSizes script from the
same directory to create a
chrom.sizes file for the UCSC database with which you are working (e.g., hg38).
Alternatively, you can download the
chrom.sizes file for any assembly hosted at UCSC from our
downloads page (click on "Full
@@ -99,31 +108,31 @@
Step 7. Move the newly created bigMaf file (bigMaf.bb) to a web-accessible http, https or ftp location. If you generated the bigMafSummary.bb and/or bigMafFrames.bb files, move those to a web accessible location, likely same location as the bigMaf.bb file.
Step 8. Construct a custom track using a single track line. Note that any of the track attributes listed here are applicable to tracks of type bigBed. The most basic version of the track line will look something like this:
track type=bigMaf name="My Big MAF" description="A Multiple Alignment" bigDataUrl=http://myorg.edu/mylab/bigMaf.bbStep 9. Paste the custom track line into the text box on the custom track -management page.
+management page. Navigate to chr22_KI270731v1_random to see the example data for this track.
The bedToBigBed program can be run with several additional options. For a full
list of the available options, type bedToBigBed (with no arguments) on the command line
to display the usage message.
In this example, you will create a bigMaf custom track using an existing bigMaf file, bigMaf.bb, located on the UCSC Genome Browser http server. This file contains data for the hg38 assembly.
To create a custom track using this bigMaf file: