2c3972fb3e23b41e21a31fd55f8ee0eb483bdabf lrnassar Tue Aug 13 08:59:32 2019 -0700 Adding FAQ entry for _alt _fix seqs and adding links from icPCR and hgBLAT refs #23291 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index b89ef79..6c8d387 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -1,29 +1,31 @@ <!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 +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> <a href="index.html">Return to FAQ Table of Contents</a></p> @@ -91,30 +93,49 @@ The online version of Blat masks 11mers from the query that occur more than 1024 times in the 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> +<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" +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 query the BLAT tool or do large batch queries. Program-driven use of BLAT is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day. Please limit batch queries to 25 sequences or less.</p> <p> For users with high-volume Blat demands, we recommend downloading the BLAT tool for local use. For more information, see <a href="#blat3">Downloading BLAT source and documentation</a>.</p> <a name="blat3"></a> <h2>Downloading Blat source and documentation</h2>