ef238e6ab90d807a28fc144fa520b50c0d1b9801 mspeir Mon Nov 3 17:12:17 2025 -0800 changing genome-source to github references, refs #35031 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 35632d8b04b..705593db630 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -253,38 +253,38 @@ <p> In summary, if you are not finding certain sequences and can afford the extra processing time, you may want to run BLAT without the <em>11.ooc</em> file if your particular situation warrants its use.</p> <a name="blat4"></a> <h2>Replicating web-based Blat percent identity and score calculations</h2> <h6>Using my own command-line Blat server, how can I replicate the percent identity and score calculations produced by web-based Blat?</h6> <p> There is no option to command-line Blat that gives you the percent ID and the score. However, we have created scripts that include the calculations: </p> <ul> <li> View the perl script from the source tree: - <a href="http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/utils/pslScore/pslScore.pl"> + <a href="http://github.com/ucscGenomeBrowser/kent/raw/master/src/utils/pslScore/pslScore.pl"> <code>pslScore.pl</code></a></li> <li> View the corresponding C program: - <a href="http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/utils/pslScore/pslScore.c"> + <a href="http://github.com/ucscGenomeBrowser/kent/raw/master/src/utils/pslScore/pslScore.c"> <code>pslScore.c</code></a> and associated library functions <code>pslScore</code> and <code>pslCalcMilliBad</code> in - <a href="http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/lib/psl.c"> + <a href="http://github.com/ucscGenomeBrowser/kent/raw/master/src/lib/psl.c"> <code>psl.c</code></a></li> </ul> <p> See our <a href="FAQlicense.html">FAQ</a> on source code licensing and downloads for information on obtaining the source.</p> <a name="blat7"></a> <h2>Replicating web-based Blat "I'm feeling lucky" search results</h2> <h6>How do I generate the same search results as web-based Blat's "I'm feeling lucky" option using command-line Blat?</h6> <p> The code for the "I'm feeling lucky" Blat search orders the results based on the sort output option that you selected on the query page. It then returns the highest-scoring alignment of the first query sequence.</p> <p>