936744a8d9b855bfda585a0e4b25c8150c6e50b2 dschmelt Mon Jan 13 13:50:10 2020 -0800 Fixing capitalization for CR #24762 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index b88c3ef..f45f743 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -403,31 +403,31 @@ <p> For example, if two 11-base tile hits align perfectly, it would result in a score of 22. This is above the minimum required score of 20 (see <a href="#blat9">Blat ALL genomes</a>), and would be reported as an alignment. However, there are penalties for gaps and mismatches, as well as potential overlap (see stepsize in <a href="../goldenPath/help/blatSpec.html">BLAT specifications</a>), all 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 +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/ ./ #For MacOS rsync -a rsync://hgdownload.soe.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