c14f12b1a0e0b239f22561f8b9eccdd668e39c94 brianlee Wed Feb 17 10:30:23 2021 -0800 Removing extra tags found by htmlCheck validate on the bigMaf help page. diff --git src/hg/htdocs/goldenPath/help/bigMaf.html src/hg/htdocs/goldenPath/help/bigMaf.html index f4c3bd0..a4610c9 100755 --- src/hg/htdocs/goldenPath/help/bigMaf.html +++ src/hg/htdocs/goldenPath/help/bigMaf.html @@ -146,31 +146,31 @@ Paste the track line into the custom track management page for the human assembly hg38 (Dec. 2013).
  • Click the "submit" button.

    • Note that additional track line options exist that are specific to the MAF format. For instance, adding the parameter setting speciesOrder="panTro4 rheMac3 mm10 rn5 canFam3 monDom5" to the above example will specify the order of sequences by species.

    Custom tracks can also be loaded via one URL line. This link loads the same bigMaf.bb track and sets additional display parameters in the URL:

    -
    http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22_KI270731v1_random&hgct_customText=track%20type=bigMaf%20name=Example%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMaf.bb%20visibility=pack
    +
    http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22_KI270731v1_random&hgct_customText=track%20type=bigMaf%20name=Example%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMaf.bb%20visibility=pack

    After this example bigMaf is loaded in the Genome Browser, click into an alignment on the browser's track display. Note that the details page displays information about the individual alignments, 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.

    1. Save the bed3+1 example file, bigMaf.txt, to your computer (Step 6, above).
    2. Save the autoSql file bigMaf.as to your computer