1a02f1ea718003c05a9e29bd233029a81fc68bc5 dschmelt Thu Jul 9 15:45:26 2020 -0700 Clarifying baseColorDefault #25868 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index 60ab3d5..8346a35 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -129,52 +129,57 @@
  • 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.

    -

    Example #2: Display Amino Acids

    +

    Example #2: Display Amino Acids and Codon Numbers

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

    1. - On the bottom of the gene details page, click the "Go to User Track track controls" link.
      2. + Access the track configuration page by right-clicking track and clicking + "Configure User Track" or alternately, from + the bottom of a gene's details page, click the "Go to User Track track + controls" link.
    2. - Change the "Color track by codons:" option from "OFF" to "genomic - codons" and change the display mode to "full". Then click - . + Making sure the display is in pack or full, change the "Color track by codons:" + option from "OFF" to "genomic + codons". Then click + or .
    3. 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.
    4. - Return to the track controls page and click the box next to "Show codon numbering", + Return to the track configuration page and check the box next to "Show codon numbering", then click . The Browser tracks display will now show amino acid - letters and numbering.
      5. + letters and codon numbering when sufficiently zoomed in.

    -Alternatively, you can also add a parameter in the custom track line, baseColorDefault=genomicCodons, -to set amino acids to display by default:

    +Alternatively, you can also add a parameter in the custom track line, +baseColorDefault=genomicCodons, +to set amino acids and codon numbering 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 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.