69ac30b5980933366818fb35e8dde865307d2613 dschmelt Wed Apr 17 16:44:38 2019 -0700 Modified paths and links for #21582, #16081 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index e372b0b..a9c79d5 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -230,31 +230,32 @@ Convert your text bigGenePred to a binary indexed format. <pre><code>bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as bigGenePredEx4.txt hg38.chrom.sizes bigGenePredEx4.bb</code></pre></li> <li> Put your binary indexed file in a web-accessible location. See the <a href="https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting">hosting section</a> for more information.</li> <li> 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. <pre> <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr19:44905790-44909388&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredEx4.bb">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr19:44905790-44909388&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredEx4.bb</a></pre> You can also add your data in the <a href="../../cgi-bin/hgCustom?db=hg38">custom track management page</a>. 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 this options using <code>baseColorDefault=genomicCodons</code> as is done below. <pre><code>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</code></pre></li> +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</code></pre> +Once you are done, you should have a track on the Genome Browser like the one below.</li> </ol> <p class='text-center'> <img class='text-center' src="../../images/bigGenePredEx4.png" alt="An image of a bigGenePred track on the browser" width="999"> </p> <h2>Sharing your data with others</h2> <p> 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 <a href="customTrack.html#EXAMPLE6">Example #6</a> on the custom track help page.</p> <h2>Extracting data from bigBed format</h2> <p> 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