d72e7b928398ec7646a62ac0a1590e3231325543 dschmelt Mon Apr 15 17:06:11 2019 -0700 Updating examples #21582 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index d911d7e..276a79c 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -108,58 +108,58 @@ track line. Note that any of the track attributes listed here are applicable to tracks of type bigBed. The basic version of the track line will look something like this:

track type=bigGenePred name="My Big GenePred" description="A Gene Set Built from Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigGenePred.bb

Step 7. Paste this custom track line into the text box on the custom track management page.

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.

Examples

-

Example #1

+

Example #1: Create Custom Track

In this example, you will create a bigGenePred custom track using a bigGenePred file located on the UCSC Genome Browser http server, bigGenePred.bb. This file contains data for the hg38 assembly.

To create a custom track using this bigGenePred file:

  1. Construct a track line that references the hosted file:

    track type=bigGenePred name="bigGenePred Example One" description="A bigGenePred file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb
  2. Paste the track line into the custom track management page for the human assembly hg38 (Dec. 2013).
  3. Click the button.

Custom tracks can also be loaded via one URL line. The link below loads the same bigGenePred track and sets additional parameters in the URL:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track&type=bigGenePred&bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb

After this example bigGenePred track is loaded in the Genome Browser, click on a gene in the browser's track display to view the details page for that gene. Note that the page offers links to several sequence types, including translated protein, predicted mRNA, and genomic sequence.

-

Example #2

+

Example #2: Display Amino Acids

In this example, you will configure the bigGenePred track loaded in Example #1 to display codons and amino acid numbering:

  1. On the bottom of the gene details page, click the "Go to ... track controls" link.
  2. Change the "Color track by codons:" option from "OFF" to "genomic codons" and check that the display mode is set to "full". Then click .
  3. On the Genome Browser tracks display, zoom to a track region where amino acids display, such as chr9:133,255,650-133,255,700, and note that the track now displays codons.
  4. Return to the track controls page and click the box next to "Show codon numbering", @@ -168,96 +168,97 @@ The browser tracks display will now show amino acid numbering.

You can also add a parameter in the custom track line, baseColorDefault=genomicCodons, to set display codons by default:

browser position chr10:67,884,600-67,884,900
 track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Two" description="A bigGenePred file" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb

Paste the above into the hg38 custom track management page to view an example of bigGenePred amino acid display at the beginning of the SIRT1 gene on chromosome 10.

An image of a track with codons colored

-

Example #3

+

Example #3: Pre-bigGenePred to BigGenePred

-In this example, you will create your own bigGenePred file from an existing bigGenePred input +In this example, you will create your own bigGenePred file from an existing pre-bigGenePred input file.

  1. Save the example bed12+8 input file to your computer, bigGenePred.txt.
  2. Download the bedToBigBed utility (Step 2, in the Creating a bigGenePred section above).
  3. Save the hg38.chrom.sizes text file to your computer. This file contains the chrom.sizes for the human hg38 assembly (Step 3, above).
  4. Save the autoSql file bigGenePred.as to your computer.
  5. Run the bedToBigBed utility to create the bigGenePred output file (step 4, above): 
    bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as bigGenePred.txt hg38.chrom.sizes bigGenePred.bb
  6. Place the newly created bigGenePred file (bigGenePred.bb) on a web-accessible server (Step 5, above).
  7. Construct a track line that points to the bigGenePred file (Step 6, above).
  8. Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (step 7, above).
-

Example #4

+

Example #4: GTF to BigGenePred

In this example, you will convert a GTF file to bigGenePred using command line utilities. You will need gtfToGenePred, genePredTobigGenePred, and bedToBigBed. You can download utilities from the utilities directory.

  1. Obtain a GTF file using the wget command. Skip this step if you already have a GTF file. 
    wget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredExample4.gtf
  2. Convert the GTF file to genePred extended format using the gtfToGenePred command. 
    gtfToGenePred -genePredExt bigGenePredExample4.gtf example4.genePred
  3. Convert the genePred extended file to a pre-bigGenePred text file. - 
    genePredToBigGenePred example4.genePred bigGenePred.txt
    4. + 
    genePredToBigGenePred example4.genePred bigGenePredEx4.txt
  4. Obtain helper files for the conversion from pre-bigGenePred to binary bigGenePred. 
    wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
 wget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.as
  5. Convert your text bigGenePred to a binary indexed format. - 
    bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as ex4BigGenePred.txt hg38.chrom.sizes bigGenePred.bb
    6. + 
    bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as bigGenePredEx4.txt hg38.chrom.sizes bigGenePredEx4.bb
  6. Put your binary indexed file in a web-accessible location. See the hosting section for more information.
  7. - View your dataset in the Browser by entering your hosted data URL in the bigDataUrl field of the - URL. For example, you can paste this link into your web browser. -
     http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb
    + 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&type=bigGenePred&bigDataUrl=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 these options using the baseColorDefault=genomicCodons code as is done below. -
    browser position chr19:44905795-44909393 
-track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Four" description="BGP Made from genePred" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb
    8. +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="BGP Made from genePred" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredEx4.bb

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.

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.