0ba2642619c71f7423c613ab0b389d9a087698b7 brianlee Tue May 24 07:24:52 2022 -0700 Fixing typo Code Review refs #29481 diff --git src/hg/htdocs/goldenPath/help/twoBit.html src/hg/htdocs/goldenPath/help/twoBit.html index fe0c6a4..2fa2f16 100755 --- src/hg/htdocs/goldenPath/help/twoBit.html +++ src/hg/htdocs/goldenPath/help/twoBit.html @@ -27,31 +27,31 @@ <pre><code> faToTwoBit genome.fa genome.2bit</code></pre></li> <li> Use <code>twoBitInfo</code> to verify the sequences in this assembly and create a chrom.sizes file, which is useful to construct the big* files in later processing steps:<br> <pre><code> twoBitInfo genome.2bit stdout | sort -k2rn > genome.chrom.sizes</code></pre></li> </ol> <p> The twoBit commands can function with the .2bit file as a URL: <pre><code> twoBitInfo -udcDir=. http://your-website.edu/~user/genome.2bit | sort -k2nr > genome.chrom.sizes</code></pre></p> <p> Sequence can be extracted from the .2bit file with the <code>twoBitToFa</code> command, for example: <pre><code> twoBitToFa -seq=chr1 -udcDir=. http://your-website.edu/~user/genome.2bit stdout > genome.chr1.fa</code></pre></p> <h3 id=extract>Examples of extracting sequences</h3> <p> -See these series of of blog posts about <a href="http://genome.ucsc.edu/blog/?s=programmatic" +See these series of blog posts about <a href="http://genome.ucsc.edu/blog/?s=programmatic" target="_blank">Accessing the Genome Browser Programmatically</a> to see examples of extracting sequences remotely, such as the following: <pre> $ twoBitToFa http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit:chr1:100100-100200 stdout >chr1:100100-100200 gcctagtacagactctccctgcagatgaaattatatgggatgctaaatta taatgagaacaatgtttggtgagccaaaactacaacaagggaagctaatt </pre></p> <p> Also, see the <a href="api.html#getData_examples" target="_blank">API getData functions</a> to see examples of using the URL, such as the following:</p> <p> <a href="https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chr1;start=100100;end=100200" target="_blank">https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chr1;start=100100;end=100200</a> <pre>