7bac7ad656d887ac590f13743461a5e676dbb89f max Fri Apr 21 02:43:57 2023 -0700 doc fixes around bigDataIndex, no redmine, galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3 diff --git src/hg/htdocs/goldenPath/help/bigBed.html src/hg/htdocs/goldenPath/help/bigBed.html index f188aae..1af394d 100755 --- src/hg/htdocs/goldenPath/help/bigBed.html +++ src/hg/htdocs/goldenPath/help/bigBed.html @@ -94,30 +94,38 @@ <strong>Step 3.</strong> Use the <code>fetchChromSizes</code> script from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">same directory</a> to create the <em>chrom.sizes</em> file for the UCSC database you are working with (e.g., hg19). If the assembly <code>genNom</code> is hosted by UCSC, chrom.sizes can be a URL like: <code>http://hgdownload.soe.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes</code>. </p> <p> <strong>Step 4.</strong> Use the <code>bedToBigBed</code> utility to create a bigBed file from your sorted BED file, using the <em>input.bed</em> file and <em>chrom.sizes</em> files created in <em>Steps 1</em> and <em>3</em>:</p> <pre><code><strong>bedToBigBed</strong> input.bed chrom.sizes myBigBed.bb</code></pre> <p> +The chrom.sizes file can also be a <em>2bit</em> or a <em>chromAlias</em> bigBed file using the +following command-line arguments: +<pre> + -sizesIs2Bit -- If set, the chrom.sizes file is assumed to be a 2bit file. + -sizesIsChromAliasBb -- If set, then chrom.sizes file is assumed to be a chromAlias + bigBed file or a URL to a such a file +</pre></p> +<p> <strong>Step 5.</strong> Move the newly created bigBed file (<em>myBigBed.bb</em>) to a web-accessible http, https, or ftp location. At this point you should have a URL to your data, such as "https://institution.edu/myBigBed.bb", and the file should be accessible outside of your institution/hosting providers network. For more information on where to host your data, please see the <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation.</p> <p> <strong>Step 6.</strong> If the file name ends with a <em>.bigBed</em> or <em>.bb</em> suffix, you can paste the URL of the file directly into the <a href="../../cgi-bin/hgCustom">custom track</a> management page, click "submit" and view the file as a track in the Genome Browser. By default, the file name will be used to name the track. To configure the track name and descriptions, you must create a "<a href="hgTracksHelp.html#TRACK">track line</a>", as shown in Example 1 Configuration <em>Step 1</em>.</p> <p> Alternatively, if you want to set the track labels and other options yourself, construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single track line. Note that any of the track attributes listed