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
+wget http://hgdownload.gi.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
+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
+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
+downloads page (click on "Full
data set" for any assembly). For example, the hg38.chrom.sizes file for the hg38
database is located at
-http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
mafToBigMaf hg38 chr22_KI270731v1_random.maf stdout | sort -k1,1 -k2,2n > bigMaf.txt
bedToBigBed -type=bed3+1 -as=bigMaf.as -tab bigMaf.txt hg38.chrom.sizes bigMaf.bb Note that the hg38 in the mafToBigMaf hg38 command indicates the referenceDb and matches the expected prefix of the primary species' sequence name, for instance hg38 for the hg38.chr22_KI270731v1_random found in the input example chr22_KI270731v1_random.maf file.
Step 6. Follow the below steps to create the binary indexed mafFrames and mafSummary files to accompany your bigMaf file:
genePredSingleCover chr22_KI270731v1_random.gp single.gp
genePredToMafFrames hg38 chr22_KI270731v1_random.maf bigMafFrames.txt hg38 single.gp
bedToBigBed -type=bed3+8 -as=mafFrames.as -tab bigMafFrames.txt hg38.chrom.sizes bigMafFrames.bb
hgLoadMafSummary -minSeqSize=1 -test hg38 bigMafSummary chr22_KI270731v1_random.maf
cut -f2- bigMafSummary.tab | sort -k1,1 -k2,2n > bigMafSummary.bed
@@ -222,66 +222,66 @@
similar to that which is available for a standard MAF track.
Example #2
In this example, you will create a bigMaf file from an existing bigMaf input file,
bigMaf.txt, located on the UCSC Genome Browser http server.
-
Save the bed3+1 example file, bigMaf.txt, to your
computer (Step 6, above).
-
Save the autoSql file bigMaf.as to your computer
(Step 3, above).
-
Download the
-
bedToBigBed utility
+ bedToBigBed utility
(Step 4, above).
-
Save the hg38.chrom.sizes text file to your computer.
This file contains the chrom.sizes for the human (hg38) assembly (Step 5, above).
-
Run the
bedToBigBed utility to create a binary indexed MAF file (Step 6,
above):
bedToBigBed -type=bed3+1 -tab -as=bigMaf.as bigMaf.txt hg38.chrom.sizes bigMaf.bb
-
Move the newly created bigMaf file (bigMaf.bb) to a web-accessible location (Step
7, above).
-
Construct a track line that points to the bigMaf file (Step 8, above).
-
Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser
(step 9, above).
Sharing your data with others
If you would like to share your bigMaf data track with a colleague, learn how to create a URL by
looking at Example 6 on this page.
Extracting data from the bigMaf format
Because bigMaf 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.
+binary utilities directory.
-
bigBedToBed — converts a bigBed file to ASCII BED format.
-
bigBedSummary — extracts summary information from a bigBed file.
-
bigBedInfo — prints out information about a bigBed file.
As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the
command line to view the usage statement.
Troubleshooting
If you encounter an error when you run the bedToBigBed program, check your input
file for data coordinates that extend past the the end of the chromosome. If these are present, run
the bedClip program
-(available here) to remove the problematic
+(available here) to remove the problematic
row(s) in your input file before running the bedToBigBed program.