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 @@
    faToTwoBit genome.fa genome.2bit
  • Use twoBitInfo 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:
        twoBitInfo genome.2bit stdout | sort -k2rn > genome.chrom.sizes
  • The twoBit commands can function with the .2bit file as a URL:

        twoBitInfo -udcDir=. http://your-website.edu/~user/genome.2bit | sort -k2nr > genome.chrom.sizes

    Sequence can be extracted from the .2bit file with the twoBitToFa command, for example:

        twoBitToFa -seq=chr1 -udcDir=. http://your-website.edu/~user/genome.2bit stdout > genome.chr1.fa

    Examples of extracting sequences

    -See these series of of blog posts about Accessing the Genome Browser Programmatically to see examples of extracting sequences remotely, such as the following:

     $ twoBitToFa http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit:chr1:100100-100200 stdout
     >chr1:100100-100200
     gcctagtacagactctccctgcagatgaaattatatgggatgctaaatta
     taatgagaacaatgtttggtgagccaaaactacaacaagggaagctaatt
     

    Also, see the API getData functions to see examples of using the URL, such as the following:

    https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chr1;start=100100;end=100200