9f028c98d1cf65be436bd62e82ada79c4588fa2d kuhn Wed Oct 16 05:02:59 2019 -0700 added hyphen diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index a2370c7..787a50b 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -58,31 +58,31 @@ speed (no queues, response in seconds) at the price of lesser homology depth
  • the ability to submit a long list of simultaneous queries in fasta format
  • five convenient output sort options
  • a direct link into the UCSC browser
  • alignment block details in natural genomic order
  • an option to launch the alignment later as part of a custom track
  • BLAT is commonly used to look up the location of a sequence in the genome or determine the exon structure of an mRNA, but expert users can run large batch jobs and make internal parameter -sensitivity changes by installing command line Blat on their own Linux server.

    +sensitivity changes by installing command-line Blat on their own Linux server.

    Blat can't find a sequence or not all expected matches

    I can't find a sequence with Blat although I'm sure it is in the genome. Am I doing something wrong?

    First, check if you are using the correct version of the genome. For example, two versions of the human genome are currently in wide use (hg19 and hg38) and your sequence may be only in one of them. Many published articles do not specify the assembly version so trying both may be necessary.

    Very short sequences that go over a splice site in a cDNA sequence can't be found, as they are not in the genome. qPCR primers are a typical example. For these cases, try using In-Silico PCR and selecting a gene set as the target. In general, the In-Silico PCR tool is more sensitive and should be preferred for pairs of primers.