8cd442780bffa931d7e6931dbea51bb6f7da4098 brianlee Wed Aug 28 13:47:14 2019 -0700 Adding chr_alt chr_fix mention in FAQ title now linked from BLAT/PCR refs #23201 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 6c8d387..a2370c7 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -1,30 +1,30 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <body> <h1>Frequently Asked Questions: BLAT</h1> <h2>Topics</h2> <ul> <li><a href="#blat1">BLAT vs. BLAST</a></li> <li><a href="#blat1b">Blat cannot find a sequence at all or not all expected matches</a></li> -<li><a href="#blat1c">Blat or In-Silico PCR finds multiple matches even though only one is +<li><a href="#blat1c">Blat or In-Silico PCR finds multiple matches such as chr_alt or chr_fix even though only one is expected</a></li> <li><a href="#blat2">BLAT use restrictions</a></li> <li><a href="#blat3">Downloading Blat source and documentation</a></li> <li><a href="#blat5">Replicating web-based Blat parameters in command-line version</a></li> <li><a href="#blat6">Using the <em>-ooc</em> flag</a></li> <li><a href="#blat4">Replicating web-based Blat percent identity and score calculations</a></li> <li><a href="#blat7">Replicating web-based Blat "I'm feeling lucky" search results</a></li> <li><a href="#blat8">Using Blat for short sequences with maximum sensitivity</a></li> <li><a href="#blat9">Blat ALL genomes</a></li> <li><a href="#blat10">Blat ALL genomes: No matches found</a></li> </ul> <hr> <p> @@ -94,31 +94,31 @@ genome. This is done to improve speed, but may result in missed hits when you are searching for sequences in repeats.</p> <p> If your input sequence is not one of the very repetitive sequences, but still present a few dozen times on a chromosome, note that Blat results are limited to 16 results per chromosome strand. This means that at most 32 locations per chromosome are returned. </p> <p> To find all matches for repetitive sequences with the online version of Blat, you can add more flanking sequence to your query. 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 <a href="#blat3">Downloading BLAT source and documentation</a> for more information.</p> <a name="blat1c"></a> -<h2>Blat or In-Silico PCR finds multiple matches even though only one is expected</h2> +<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 assmeblies, 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 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"