574532b972ccb3d1ee900ccfb000782ffd0b6a2d dschmelt Thu Aug 8 16:07:02 2019 -0700 Fixing typo for code reviewq #23955 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 8971b7b..b89ef79 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -149,31 +149,31 @@ <p> <em>standalone Blat</em>:</p> <ul> <li>Blat search:<br> <code>blat -stepSize=5 -repMatch=2253 -minScore=20 -minIdentity=0 database.2bit query.fa output.psl </code><br></li> <li><strong>Note:</strong> To replicate web results, PSL output should be used. BLAT handles alternative output formats (such as blast8) slightly differently, and this can lead to minor differences in results; particularly for short alignments. Furthermore, the query sequence should have all U nucleotides converted to T nucleotides or have the "-q=rna" flag used to match the web-Blat.</li> </ul> <p> <em>faToTwoBit</em>:</p> <ul> - <li>Uses soft masking to converst Fasta format to the 2bit format for Blat input.</li> + <li>Uses soft masking to convert Fasta format to the 2bit format for Blat input.</li> </ul> <p> <em>gfServer</em> (this is how the UCSC web-based Blat servers are configured): <ul> <li> Blat server (capable of PCR):<br> <code>gfServer start blatMachine portX -stepSize=5 -log=untrans.log database.2bit</code></li> <li> translated Blat server:<br> <code>gfServer start blatMachine portY -trans -mask -log=trans.log database.2bit</code> </li> </ul> <p>For enabling DNA/DNA and DNA/RNA matches, only the host, port and twoBit files are needed. The same port is used for both untranslated BLAT (gfClient) and PCR (webPcr). You'll need a separate