bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 6c6e6778a22..35632d8b04b 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -141,33 +141,33 @@ of one hit every 15 seconds and no more than 5,000 hits per day. Please limit batch queries to 25 sequences or less.</p> <p> For users with high-volume Blat demands, we recommend downloading the BLAT tool for local use. For more information, see <a href="#blat3">Downloading BLAT source and documentation</a>.</p> <a name="blat3"></a> <h2>Downloading BLAT source and documentation</h2> <h6>Is the BLAT source available for download? Is documentation available?</h6> <p> BLAT source and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the <a href="http://www.kentinformatics.com" target="_blank">Kent Informatics website</a>.</p> <p> BLAT source may be downloaded from -<a href="http://hgdownload.soe.ucsc.edu/admin/">http://hgdownload.soe.ucsc.edu/admin/</a> (located +<a href="http://hgdownload.gi.ucsc.edu/admin/">http://hgdownload.gi.ucsc.edu/admin/</a> (located at /kent/src/blat within the most recent jksrci*.zip source tree). For BLAT executables, go to -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">http://hgdownload.soe.ucsc.edu/admin/exe/</a> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">http://hgdownload.gi.ucsc.edu/admin/exe/</a> and choose your machine type.</p> <p> Documentation on BLAT program specifications is available <a href="../goldenPath/help/blatSpec.html">here</a>. Note that the command-line BLAT does not return matches to U nucleotides in the query sequence.</p> <a name="blat5"></a> <h2>Replicating web-based Blat parameters in command-line version</h2> <h6>I'm setting up my own Blat server and would like to use the same parameter values that the UCSC web-based Blat server uses.</h6> <p> We almost always <strong>expect small differences</strong> between the hgBLAT/gfServer and the stand-alone, command-line Blat. The best matches can be found using pslReps and pslCDnaFilter utilities. The web-based Blat is tuned permissively with a minimum cut-off score of 20, which will display most of the alignments. We advise deciding which @@ -417,41 +417,41 @@ of which could bring the score below 20. In that case, Blat ALL would report 2 "hits", but clicking into the assembly would report no matches. This most often occurs when there are only a few (1-3) hits reported by Blat ALL.</p> <a name="blat11"></a> <h2>Approximating web-based Blat results using gfServer/gfClient</h2> <p> Often times using the gfServer/gfClient provides a better approximation or even replicate of the web-based Blat results, which otherwise cannot be found using standalone Blat. This approach mimics the Blat server used by the Genome Browser web-based Blat. The following example will show how to set up an hg19 gfServer, then make a query. First, download the appropriate utility for the operating system and give it executable permissions:</p> <pre> #For linux -rsync -a rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/blat/ ./ +rsync -a rsync://hgdownload.gi.ucsc.edu/genome/admin/exe/linux.x86_64/blat/ ./ #For MacOS -rsync -a rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.x86_64/blat/ ./ +rsync -a rsync://hgdownload.gi.ucsc.edu/genome/admin/exe/macOSX.x86_64/blat/ ./ chmod +x gfServer gfClient blat </pre> <p> Next, download the appropriate .2bit genome (hg19 in this example), and run the gfServer utility with the web Blat parameters, designating the local machine and port 1234:</p> <pre> -wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit +wget http://hgdownload.gi.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit ./gfServer start 127.0.0.1 1234 -stepSize=5 hg19.2bit </pre> <p> After a few moments, the gfServer will initialize and be ready to recieve queries. In order to approximate web Blat, we will use the gfClient with the following parameters, designating our input and output files.</p> <pre> ./gfClient -minScore=20 -minIdentity=0 127.0.0.1 1234 . input.fa out.psl </pre> <p>The output file <code>out.psl</code> should have results very similar to web-based Blat.</p> <a name="blat12"></a> <h2>Standalone or gfServer/gfClient result start positions off by one</h2> <h6>My standalone Blat results or gfServer/gfClient Blat results have a start position that is one less that what I see on web Blat results</h6> @@ -498,43 +498,43 @@ <p> Query types include DNA, protein, translated RNA and translated DNA:</p> <pre> <a href="https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=GACCTCGGCGTGGCCTAGCG&type=DNA&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=GACCTCGGCGTGGCCTAGCG&type=DNA&db=hg38&output=json</a> <a href="https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNM&type=protein&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNM&type=protein&db=hg38&output=json</a> <a href="https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=UUUCCCUUCCCCACUGUAGUGGGAGAGAAGGGAGUGGCCAUACCAUAUUUUUCUCGUGGGCCGUUGUAGUCAUAAGGCCUUCCUUUGCGGAAAAUUUUCAGGGUGGGAUA&type=translated%20RNA&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=UUUCCCUUCCCCACUGUAGUGGGAGAGAAGGGAGUGGCCAUACCAUAUUUUUCUCGUGGGCCGUUGUAGUCAUAAGGCCUUCCUUUGCGGAAAAUUUUCAGGGUGGGAUA&type=translated%20RNA&db=hg38&output=json</a> <a href="https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=TTTCCCTTCCCCACTGTAGTGGGAGAGAAGGGAGTGGCCATACCATATTTTTCTCGTGGGCCGTTGTAGTCATAAGGCCTTCCTTTGCGGAAAATTTTCAGGGTGGGATA&type=translated%20DNA&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=TTTCCCTTCCCCACTGTAGTGGGAGAGAAGGGAGTGGCCATACCATATTTTTCTCGTGGGCCGTTGTAGTCATAAGGCCTTCCTTTGCGGAAAATTTTCAGGGTGGGATA&type=translated%20DNA&db=hg38&output=json</a> </pre> <a name="blat15"></a> <h2>Running BLAT Locally</h2> <h6>How do I run BLAT locally if I'm running into limitations with the web-based version?</h6> <p> If you have access to a Linux or Mac OSX command-line you can run <code>blat</code> locally. The blat binary is available under the directory for your system type under the -<a href="https://hgdownload.soe.ucsc.edu/admin/exe/">utilities directory</a> on our download server. +<a href="https://hgdownload.gi.ucsc.edu/admin/exe/">utilities directory</a> on our download server. <p> Once you have the downloaded the <code>blat</code> program to your computer, ensure the 'execute' bit is on for permissions: <pre><code>$ ls -og blat -rwxrwxr-x 1 5528712 Nov 7 04:03 blat </code></pre> <p> If the permissions indicate something like: <code>-rw-rw-r--</code>, then you will need to enable the ability to execute the program: <pre><code>$ chmod +x blat</code></pre> <p> To confirm that it works, run the program without arguments. This will also display the help message. <pre><code>$ ./blat</code></pre> <p> You can now use this program locally on your sequences. For example, given a sample.fa, to find that sequence in the human/hg38 genome, you would run: <pre><code>$ ./blat hg38.2bit sample.fa output.psl</code></pre> <p> You can download the 2bit file for your assembly of interest from the -<a href="https://hgdownload.soe.ucsc.edu/downloads.html">download server</a> +<a href="https://hgdownload.gi.ucsc.edu/downloads.html">download server</a> under the "Genome sequence files and select annotations (2bit, GTF, GC-content, etc)" link. For example, the hg38.2bit sequence can be found <a -href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/">here</a>. +href="https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/">here</a>. <!--#include virtual="$ROOT/inc/gbPageEnd.html" --> </body>