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

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:

 wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
 ./gfServer start 127.0.0.1 1234 -stepSize=5 hg19.2bit

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.

 ./gfClient -minScore=20 -minIdentity=0 127.0.0.1 1234 . input.fa out.psl

The output file out.psl should have results very similar to web-based Blat.

Standalone or gfServer/gfClient result start positions off by one

-
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
+
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

This is due to how we store internal coordinates in the Genome Browser. The default -blat Output type of hyperlink shows results in our +Blat Output type of hyperlink shows results in our internal coordinate data structure. These internal coordinates have a zero-based start and a one-based end. See the following FAQ entry for more information.

-If the Output type is changed to psl on web blat, the same -zero-based half open coordinate results will be seen as the standalone blat and gfServer/gfClient +If the Output type is changed to psl on web Blat, the same +zero-based half open coordinate results will be seen as the standalone Blat and gfServer/gfClient procedures.