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
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
-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