a088083189a07e9d1304023f7370f27c713642c7 max Tue Dec 10 02:04:47 2019 -0800 adding note to blat FAQ after refs #24595 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 487e0f3..f93e405 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -93,31 +93,34 @@ </a>, the problem may be a result of BLAT's query-masking. This happens if your input sequence is part of a repeat and present thousands of times in the genome. 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 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 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 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