09360ed5d9de0f031b6f62924852b533c8fda23a mspeir Sat Sep 26 18:45:33 2026 -0700 Fixing typo in zip name, no refs diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index c9f5fd74f9a..836a4897d46 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -142,31 +142,31 @@ 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.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 +at /kent/src/blat within the most recent jksrc*.zip source tree). For BLAT executables, go to <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