9a8fb0ce2f54cc84130cf0eaeead2b18d17d4e70 lrnassar Fri Oct 18 10:38:06 2019 -0700 Fixing consistency and some typos based on feedback refs #24280 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 7a54f0b..eaa9e11 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -418,39 +418,39 @@ 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 ./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 apporximate web Blat we will us the gfClient with the following parameters, designating +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> +<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> <p> This is due to how we store internal coordinates in the Genome Browser. The default -blat <strong>Output type</strong> of <strong>hyperlink</strong> shows results in our +Blat <strong>Output type</strong> of <strong>hyperlink</strong> shows results in our internal coordinate data structure. These internal coordinates have a zero-based start and a one-based end. See the following <a target="_blank" href="/FAQ/FAQtracks#tracks1" >FAQ entry</a> for more information.</p> <p> -If the <strong>Output type</strong> is changed to <strong>psl</strong> on web blat, the same -zero-based half open coordinate results will be seen as the standalone blat and gfServer/gfClient +If the <strong>Output type</strong> is changed to <strong>psl</strong> on web Blat, the same +zero-based half open coordinate results will be seen as the standalone Blat and gfServer/gfClient procedures.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" --> </body>