89c380d28049d3f28fd09a897260d1ee0fbb3248 dschmelt Mon Apr 29 15:32:09 2019 -0700 Making upper case Browser for code review #23399 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index 3397494..bc5537c 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -1,291 +1,291 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser bigGenePred Track Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>bigGenePred Track Format</h1> <p> The bigGenePred format stores positional annotations for collections of exons in a compressed format, similar to how <a href="../../FAQ/FAQformat.html#format1">BED</a> files are compressed into bigBeds. The bigGenePred format includes 8 additional fields that contain details about coding frames, annotation status, and other gene-specific information. This is commonly used in the Browser to display start codons, stop codons, and amino acid translations.</p> <p> Before compression, bigGenePred files can be described as bed12+8 files. bigGenePred files can be created using the program <code>bedToBigBed</code>, run with the <code>-as</code> option to pull in a special <a href="http://www.linuxjournal.com/article/5949" target="_blank"> autoSql</a> (<em>.as</em>) file that defines the extra fields of the bigGenePred.</p> <p> Much like bigBed, bigGenePred files are in an indexed binary format. The advantage of using a binary format is that only the portions of the file needed to display a particular region are read by the Genome Browser server. Because of this, indexed binary files have much faster display performance than regular BED format files when working with large data sets. As with all big files, bigGenePred files must be hosted on a web-accessible server (http, https, or ftp) to be displayed. For more information on finding a web-accessible location to host your bigGenePred files, please see the <a href="hgTrackHubHelp.html#Hosting">hosting section</a> of the Track Hub Help documentation. </p> <a name="bigGenePred"></a> <h2>bigGenePred format description</h2> <p> The following autoSql definition specifies bigGenePred gene prediction files. This definition, contained in the file <a href="examples/bigGenePred.as"><em>bigGenePred.as</em></a>, is pulled in when the <code>bedToBigBed</code> utility is run with the <code>-as=bigGenePred.as</code> option. <pre><code>table bigGenePred "bigGenePred gene models" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name or ID of item, ideally both human-readable and unique" uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "RGB value (use R,G,B string in input file)" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts;"Start positions relative to chromStart" string name2; "Alternative/human readable name" string cdsStartStat; "Status of CDS start annotation (none, unknown, incomplete, or complete)" string cdsEndStat; "Status of CDS end annotation (none, unknown, incomplete, or complete)" int[blockCount] exonFrames; "Exon frame {0,1,2}, or -1 if no frame for exon" string type; "Transcript type" string geneName; "Primary identifier for gene" string geneName2; "Alternative/human-readable gene name" string geneType; "Gene type" ) </code></pre> <p> The following bed12+8 is an example of a <a href="examples/bigGenePred.txt">pre-bigGenePred text file </a>.</p> <h2>Creating a bigGenePred track from a bed12+8 file</h2> <p> <strong>Step 1.</strong> Format your pre-bigGenePred file. The first 12 fields of pre-bigGenePred files are described by the <a href="../../FAQ/FAQformat.html#format1">BED file format</a>. Your file must also contain the 8 extra fields described in the autoSql file definition shown above: <code>name2, cdsStartStat, cdsEndStat, exonFrames, type, geneName, geneName2, geneType</code>. For example, you can use this bed12+8 input file, <a href="examples/bigGenePred.txt">bigGenePred.txt</a>. Your pre-bigGenePred file must be sorted first on the <code>chrom</code> field, and secondarily on the <code>chromStart</code> field. You can use the UNIX <code>sort</code> command to do this:</p> <pre><code>sort -k1,1 -k2,2n unsorted.bed > input.bed</code></pre> <p> <strong>Step 2.</strong> Download the <code>bedToBigBed</code> program from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <p> <strong>Step 3.</strong> Download the <em>chrom.sizes</em> file for your assembly from our <a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloads</a> page (click on "Full data set" for your organism). For example, the <em>hg38.chrom.sizes</em> file for the hg38 database is located at <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" target="_blank">http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>. Alternatively, you can use the <code>fetchChromSizes</code> script from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utilities directory</a>. <p> <strong>Step 4.</strong> Create the bigGenePred file from your pre-bigGenePred file using the <code>bedToBigBed</code> utility command:</p> <pre><code><strong>bedToBigBed</strong> -as=bigGenePred.as -type=bed12+8 bigGenePred.txt chrom.sizes myBigGenePred.bb</code></pre> <p> <strong>Step 5.</strong> Move the newly created bigGenePred file (<em>myBigGenePred.bb</em>) to a web-accessible http, https, or ftp location. See <a href="hgTrackHubHelp.html#Hosting">hosting section</a> if necessary.</p> <p> <strong>Step 6.</strong> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. 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:</p> <pre><code>track type=bigGenePred name="My Big GenePred" description="A Gene Set Built from Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigGenePred.bb</code></pre> <p> <strong>Step 7.</strong> Paste this custom track line into the text box on the <a href="../../cgi-bin/hgCustom">custom track page</a> with your modified URL. Click <button>Submit</button> and your track should -load successfully. Then click <button>Go</button> to be taken to the browser window +load successfully. Then click <button>Go</button> to be taken to the Browser window with your custom track at the top. Note that there might not be data at all positions. </p> <h2>Examples</h2> <a name="Example1"></a> <h3>Example #1: Create a Custom Track</h3> <p> Create a bigGenePred custom track using the bigGenePred file located on the UCSC Genome Browser http server, <em>bigGenePred.bb</em>. This file contains data for the hg38 assembly.</p> <ol> <li> Construct a track line that references the hosted file:</p> <pre><code>track type=bigGenePred name="bigGenePred Example One" description="A bigGenePred file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb</code></pre> <li> Paste the track line into the <a href="../../cgi-bin/hgCustom?db=hg38">custom track page</a> for the human assembly, hg38.</li> <li> Click the <button>Submit</button> button.</li> </ol> <p> 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:</p> <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb" target="_blank"><pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb</code></pre></a> <p> 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 +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.</p> <a name="Example2"></a> <h3>Example #2: Display Amino Acids</h3> <p> In this example, you will configure the bigGenePred track loaded in Example #1 to display codons and amino acid numbering: <ol> <li> On the bottom of the gene details page, click the "Go to User Track track controls" link.</li> <li> Change the "Color track by codons:" option from "OFF" to "genomic codons" and change the display mode to "full". Then click <button>Submit</button>. <li> Zoom to a region with track data, such as <code>chr9:133,255,650-133,255,700</code>, and note that the track now displays amino acids. <li> Return to the track controls page and click the box next to "Show codon numbering", - then click <button>Submit</button>. The browser tracks display will now show amino acid + then click <button>Submit</button>. The Browser tracks display will now show amino acid letters and numbering.</li> </ol> <p> Alternatively, you can also add a parameter in the custom track line, <code>baseColorDefault=genomicCodons</code>, to set amino acids to display by default:</p> <pre><code>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 </code></pre> <p> Paste the above into the hg38 <a href="../../cgi-bin/hgCustom?db=hg38">custom track page</a> to view an example of bigGenePred amino acid display at the beginning of the SIRT1 gene on chromosome 10.</p> <p class='text-center'> <img class='text-center' src="../../images/codonColoring.png" alt="An image of a track with codons colored" width="999"> </p> <a name="Example3"></a> <h3>Example #3: Bed12+8 to BigGenePred</h3> <p> In this example, you will create your own bigGenePred file from an existing pre-bigGenePred input file, a bed12+8 file.</p> <ol> <li> Save the example bed12+8 input file to your computer, <em><a href="examples/bigGenePred.txt">bigGenePred.txt</a></em>.</li> <li> Download the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/"><code>bedToBigBed</code></a> utility (<em>Step 2</em>, in the <em>Creating a bigGenePred</em> section above).</li> <li> Save the <a href="hg38.chrom.sizes"><em>hg38.chrom.sizes</em> text file</a> to your computer. This file contains the chrom.sizes for the human hg38 assembly (<em>Step 3</em>, above).</li> <li> Save the autoSql file <a href="examples/bigGenePred.as"><em>bigGenePred.as</em></a> to your computer.</li> <li> Run the <code>bedToBigBed</code> utility to create the bigGenePred output file (<em>step 4</em>, above): <pre><code><B>bedToBigBed</B> -type=bed12+8 -tab -as=bigGenePred.as bigGenePred.txt hg38.chrom.sizes bigGenePred.bb</code></pre></li> <li> Place the newly created bigGenePred file (<em>bigGenePred.bb</em>) on a web-accessible server (<em>Step 5</em>, above).</li> <li> Construct a track line that points to the bigGenePred file (<em>Step 6</em>, above).</li> <li> Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (<em>step 7</em>, above).</li> </ol> <a name="Example4"></a> <h3>Example #4: GTF (or GFF) to BigGenePred </h3> <p>In this example, you will convert a GTF file to bigGenePred using command line utilities. You will need <code>gtfToGenePred</code>, <code>genePredTobigGenePred</code>, and <code>bedToBigBed</code>. If you would like to convert a GFF file to bigGenePred, you will use <code>gff3ToGenePred</code> in place of the <code>gtfToGenePred</code>. You can download utilities from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utilities directory</a>.</p> <ol> <li> Obtain a GTF file using the <code>wget</code> command. Skip this step if you already have a GTF or GFF file. <pre><code>wget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredExample4.gtf</code></pre></li> <li> Convert the GTF file to genePred extended format using the <code>gtfToGenePred</code> command. <pre><code>gtfToGenePred -genePredExt bigGenePredExample4.gtf example4.genePred</code></pre> If you are converting a GFF file, use the <code>gff3ToGenePred</code> command. <pre><code>gff3ToGenePred yourFile.gff example4.genePred </pre></code></li> <li> Convert the genePred extended file to a pre-bigGenePred text file. <pre><code>genePredToBigGenePred example4.genePred bigGenePredEx4.txt</code></pre></li> <li> 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 <a href="http://hgdownload.soe.ucsc.edu">downloads directory</a> under "Full data set". <pre><code>wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes wget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.as</code></pre></li> <li> 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="Ex4:BigGenePred Made from GTF" 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"> + <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 <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <ul> <li> <code>bigBedToBed</code> — converts a bigBed file to ASCII BED format.</li> <li> <code>bigBedSummary</code> — extracts summary information from a bigBed file.</li> <li> <code>bigBedInfo</code> — prints out information about a bigBed file.</li> </ul> <p> As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the command line to view the usage statement.</p> <h2>Troubleshooting</h2> <p> If you encounter an error when you run the <code>bedToBigBed</code> program, check your input file for data coordinates that extend past the end of the chromosome. If these are present, run the <code>bedClip</code> program (<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">available here</a>) to remove the problematic row(s) before running the <code>bedToBigBed</code> program. </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" --> <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser bigGenePred Track Format" --> <!--#set var="ROOT" value="../.." -->