947a8b9ea2a461b1a92629306de66e995d557c32 dschmelt Tue Apr 23 11:21:26 2019 -0700 Finishing cut off sentence, adding code tags in Ex4 #23354 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index ec10044..3397494 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -96,46 +96,49 @@ 
bedToBigBed -as=bigGenePred.as -type=bed12+8 bigGenePred.txt chrom.sizes myBigGenePred.bb

Step 5. Move the newly created bigGenePred file (myBigGenePred.bb) to a web-accessible http, https, or ftp location. See hosting section if necessary.

Step 6. Construct a custom track using a single track line. Any of the track attributes will be available for use on bigBed tracks. 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. Click and you should be taken to a

+track page with your modified URL. Click and your track should +load successfully. Then click to be taken to the browser window +with your custom track at the top. Note that there might not be data at all positions. +

Examples

Example #1: Create a Custom Track

Create a bigGenePred custom track using the bigGenePred file located on the UCSC Genome Browser http server, bigGenePred.bb. This file contains data for the hg38 assembly.

  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.
    3. + Paste the track line into the custom track + page for the human assembly, hg38.
  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%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb

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

@@ -152,31 +155,31 @@ .
  • Zoom to a region with track data, such as chr9:133,255,650-133,255,700, and note that the track now displays amino acids.
  • Return to the track controls page and click the box next to "Show codon numbering", then click . The browser tracks display will now show amino acid letters and numbering.

    • Alternatively, you can also add a parameter in the custom track line, baseColorDefault=genomicCodons, to set amino acids to display 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 +Paste the above into the hg38 custom track 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: Bed12+8 to BigGenePred

    In this example, you will create your own bigGenePred file from an existing pre-bigGenePred input file, a bed12+8 file.

    1. Save the example bed12+8 input file to your computer, bigGenePred.txt.
    2. @@ -192,42 +195,43 @@ 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
    3. Place the newly created bigGenePred file (bigGenePred.bb) on a web-accessible server (Step 5, above).
    4. Construct a track line that points to the bigGenePred file (Step 6, above).
    5. Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (step 7, above).

    Example #4: GTF (or GFF) to BigGenePred

    In this example, you will convert a GTF file to bigGenePred using command line utilities. -You will need gtfToGenePred, genePredTobigGenePred, -and bedToBigBed. If you would like to convert a GFF file to bigGenePred, you will use -gff3ToGenePred in place of the gtfToGenePred. You can download utilities from the +You will need gtfToGenePred, genePredTobigGenePred, +and bedToBigBed. If you would like to convert a GFF file to bigGenePred, you will use +gff3ToGenePred in place of the gtfToGenePred. 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 or GFF file. + Obtain a GTF file using the wget command. Skip this step if you already have a GTF + or GFF file. 
      wget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredExample4.gtf
    2. - Convert the GTF file to genePred extended format using the gtfToGenePred command. + Convert the GTF file to genePred extended format using the gtfToGenePred command. 
      gtfToGenePred -genePredExt bigGenePredExample4.gtf example4.genePred
      - If you are converting a GFF file, use the gff3ToGenePred command. + If you are converting a GFF file, use the gff3ToGenePred command. 
      gff3ToGenePred yourFile.gff example4.genePred
    3. Convert the genePred extended file to a pre-bigGenePred text file. 
      genePredToBigGenePred example4.genePred bigGenePredEx4.txt
    4. Obtain helper files for the conversion to binary bigGenePred. If you are not using hg38, you can find the chrom.sizes file for your organism in the downloads directory under "Full data set". 
      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 bigGenePredEx4.txt hg38.chrom.sizes bigGenePredEx4.bb
    6. Put your binary indexed file in a web-accessible location. See the