d5932e4051a4885f0036831cdfc5fbf1eb08a499 lrnassar Tue Oct 10 17:16:27 2023 -0700 Fixing broken blog links, refs #32439 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 2c3eda2..02a517e 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -109,31 +109,31 @@ the executables of BLAT and the .2bit file of a genome to your own machine and use BLAT on the command line. See <a href="#blat3">Downloading BLAT source and documentation</a> 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.</p> <a name="blat1c"></a> <h2>BLAT or In-Silico PCR finds multiple matches such as chr_alt or chr_fix even though only one is expected</h2> <h6>I am seeing two or more matches in the genome although there should only be one. What are these extra matches?</h6> <p> 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 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 <a -target="_blank" href="http://genome.ucsc.edu/blog/patches/">patches blog post</a> for more +target="_blank" href="https://genome-blog.gi.ucsc.edu/blog/patches/">patches blog post</a> for more information.</p> <p> 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 <a target="_blank" href="FAQdownloads#downloadAlt">FAQ entry</a> on the topic.</p> <a name="blat2"></a> <h2>BLAT usage restrictions</h2> <h6>I received a warning from your Blat server informing me that I had exceeded the server use limitations. Can you give me information on the UCSC Blat server use parameters?</h6> <p> Due to the high demand on our Blat servers, we restrict service for users who programmatically