8185d253cdfd94afeef826febda5116c29fb80d8 brianlee Mon May 13 15:13:04 2019 -0700 Adding a short new FAQ for restricted downloads and cleaning up some tag and link problems found by htmlCheck validate/checkLinks refs #23493 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index 84298db..89f83a5 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -369,31 +369,31 @@ To find transcription direction, we use a method that relies on finding gt-ag canonical pairs in one direction more often than in the opposite direction. The calculation is:</p> <pre>gt/ag introns minus ct/ac introns = intronOrientation</pre> <p> The sign of this calculated intronOrientation field (stored in the estOrientInfo table) shows the orientation of the transcript relative to the EST. Therefore, if intronOrientation is positive, then the EST appears in the display with the arrows pointing in the same direction as the EST.</p> <a name="download8"></a> <h2>Missing RefSeq ID</h2> <h6>Why isn't my refseq ID in your database?</h6> <p> It may have been added after we last downloaded data from GenBank, or it may have been replaced or removed. You can check the submission date and status of an accession on the -<a href="https://www.ncbi.nlm.nih.gov:80/entrez/" target="_blank">NCBI Entrez Nucleotide +<a href="https://www.ncbi.nlm.nih.gov/nucleotide/" target="_blank">NCBI Entrez Nucleotide site</a>.</p> <a name="download9"></a> <h2>Finished vs. draft segments</h2> <h6>Do chr<em>N</em>.fa tables contain both finished and draft segments? If so, how do you determine which segments are finished?</h6> <p> Yes, these tables contain both finished and draft segments. Use the corresponding chr<em>N</em>_gold table to look them up. The quality of the draft varies. In general, the larger the contig it is in, the better the quality. The quality of the last 500 bases on either end of a contig tends to be lower than that of the rest of the contig. <p> How do you determine the accuracy? The base-calling program <a href="http://www.phrap.org/" target="_blank">Phred</a> analyzes the traces from the sequencing machines and assigns a quality score to these. These quality scores are used by the <a href="http://www.phrap.org/" @@ -545,31 +545,31 @@ </tr> <tr> <td>2 (part)</td><td>13</td><td>2b</td> </tr> <tr> <td>3</td><td>2</td><td>3</td> </tr> <tr> <td>4</td><td>3</td><td>4</td> </tr> <tr> <td>5</td><td>4</td><td>5</td> </tr> <tr> <td>6</td><td>5</td><td>6</td> - </tr + </tr> <tr> <td>7</td><td>6</td><td>7</td> </tr> <tr> <td>8</td><td>7</td><td>8</td> </tr> <tr> <td>9</td><td>11</td><td>9</td> </tr> <tr> <td>10</td><td>8</td><td>10</td> </tr> <tr> <td>11</td><td>9</td><td>11</td> </tr> @@ -611,31 +611,31 @@ </tr> <tr> <td>Y</td><td>Y</td><td>Y</td> </tr> </table> </div> </div> <a name="download28"></a> <h2>Converting genome coordinates between assemblies</h2> <h6>I've been researching a specific area of the human genome on the current assembly, and now you've just released a new version. Is there an easy way to locate my area of interest on the new assembly?</h6> <p> You can migrate data from one assembly to another by using the <a href="../cgi-bin/hgBlat">blat</a> -alignment tool or by converting assembly coordinates</a>. There are two conversion tools available +alignment tool or by converting assembly coordinates. There are two conversion tools available on the Genome Browser web site: the Convert utility and the LiftOver tool. The Convert utility, which is accessed from the menu on the Genome Browser annotation tracks page, supports forward, reverse, and cross-species conversions, but does not accept batch input. The <a href="../cgi-bin/hgLiftOver">LiftOver</a> tool, accessed via the Utilities link on the Genome Browser home page, also supports forward, reverse, and cross-species conversions, as well as batch conversions.</p> <p> If you wish to update a large number of coordinates to a different assembly and have access to a Linux platform, you may find it useful to try the command-line version of the LiftOver tool. The executable file for this utility can be downloaded <a href="https://genome-store.ucsc.edu" target="_blank">here</a>. LiftOver requires a UCSC-generated <em>over.chain</em> file as input. Pre-generated files are available for selected assemblies from the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#liftover">Downloads</a> page. If the desired file is not available, send a request to the <a href="../contacts.html">genome mailing list</a> and @@ -857,31 +857,31 @@ </li> </ul> <p> <strong>SNP data:</strong> If queries against the SNP table on one of our public MySQL servers or on your own MySQL installation are slow, then they can be sped up by using the "bin" field; you can <a href="../contacts.html">contact us</a> for more information.</p> <p> Read more in <a href="http://genome.ucsc.edu/blog/"> our blog</a> about <a href="http://genome.ucsc.edu/blog/?s=programmatic"> Accessing the Genome Browser Programmatically</a> to acquire data. </p> <a name="download37"></a> <h2>Obtaining GTF (Gene Transfer Format)</h2> -<h6>What is the best method for obtaining GTF output?</h5> +<h6>What is the best method for obtaining GTF output?</h6> <p> Currently, the <a href="../cgi-bin/hgTables">Table Browser</a> does not have an option return data as <a href="../FAQ/FAQformat.html#format4">GTF</a> files. Currently, the best method to obtain GTF files is to use the command-line format conversion utility, <code>genePredToGtf</code>. This can be set up to automatically connect to the UCSC public SQL database and return GTF files in a few minutes using <a href="http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format#Using_kent_commands_with_the_public_database_server"> this short guide</a>.</p> <p> <p>Summary of Table Browser limitations:</p> <ul> <li>The Table Browser has transcript IDs only, so although it includes both "gene_id" and "transcript_id" fields in its output, the value for transcript ID (e.g., ENST#) is used for both fields.</li> <li>The Table Browser adds start and stop codon annotations whether or not the transcript alignment includes proper start and stop codons.</li> @@ -919,16 +919,25 @@ <h2>'Permisssion denied' error when trying to use command-line utilities</h2> <h6>Why do I get a 'Permission denied' error when I try to run command-line utilities?</h6> <p> In order for your computer to run a freshly downloaded utility, you will need to update the file system permissions to allow your operating system to run the program. <br> To make utilities usable, turn on its 'executable' bit: <pre> <code>$ chmod +x ./filePath </code></pre> <pre> <code>$ ./filePath/utility_name</code></pre> Example: <pre><code>$ chmod +x /home/user/liftover/liftOver</code></pre> See also: <a href="http://en.wikipedia.org/wiki/Chmod" target="_blank">http://en.wikipedia.org/wiki/Chmod</a> </p> +<a name="download40"></a> +<h2>Restricted Track Data</h2> +<h6>Why can I not download some data in the Table Browser or find the download files?</h6> +<p> +Some data is provided by external groups and is not available for download or mirroring +by any third party without the permission of the owners, such as the OMIM track data, which +is the property of Johns Hopkins University. +</p> + <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->