198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 705593db630..c9f5fd74f9a 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -106,31 +106,31 @@ if your sequence is less than 30 bp. You can work around this minimum length limitation by adding more flanking sequence to your query to make the query unique enough. If this is not possible, the only alternative is to download the executables of BLAT and the .2bit file of a genome to your own machine and use BLAT on the command line. See Downloading BLAT source and documentation for more information. When using the command line version of BLAT, you can set the repMatch option to a large value to try to improve finding matches in repetitive regions and do not use one of the default 11.ooc repeat masking files.

BLAT or In-Silico PCR finds multiple matches such as chr_alt or chr_fix even though only one is expected

I am seeing two or more matches in the genome although there should only be one. What are these extra matches?

This usually occurs on the newer genome assemblies, such as hg38, when you search a sequence that -has an "alternate" or "fix" sequence. To improve the quality of the these +has an "alternate" or "fix" sequence. To improve the quality of these assemblies, curators have added multiple versions of some important loci, e.g. the MHC regions. They also add fix sequences to resolve errors without changing the reference. See our patches blog post for more information.

When you blat or isPCR a sequence which matches a chromosome location that also has a fix or alt sequence, you will see a match on the reference chromosome (e.g. "chr1") and another match on the patch sequence (e.g. chr1_KN196472v1_fix). In most cases it is safe to ignore the patch hit, as a human genome will not contain both the reference and alternate sequence at the same time. For more information on the specific kinds of patch sequences see our FAQ entry on the topic.

BLAT usage restrictions

I received a warning from your Blat server informing me that I had exceeded the server use @@ -431,42 +431,42 @@ #For linux rsync -a rsync://hgdownload.gi.ucsc.edu/genome/admin/exe/linux.x86_64/blat/ ./ #For MacOS rsync -a rsync://hgdownload.gi.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.gi.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 +After a few moments, the gfServer will initialize and be ready to receive queries. In order 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

+position that is one less than 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 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 procedures.

Protein-translated BLAT having different results

Protein-translated BLAT (protein or translated RNA queries) uses the standard vertebrate