f60458991e24e246fd061ca1d4e6861585b0cd09 dschmelt Mon Apr 8 15:14:12 2019 -0700 Fixing minor things for code review #23271 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index d5f405b..8e1c758 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -203,31 +203,31 @@ Place the newly created bigGenePred file (bigGenePred.bb) on a web-accessible server (Step 5, above).
  • Construct a track line that points to the bigGenePred file (Step 6, above).
  • Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (step 7, above).

    • Example #4

    In this example, you will convert a genePred file to bigGenePred using command line utilities. You can download utilities from the utilities directory.

    1. - Obtain a genePred extended file. Here we are downloading the Comprehensive Gencode V28 gene data. + Obtain a genePred extended file. In this example, we are downloading the Comprehensive Gencode V28 gene data. 
      wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgEncodeGencodeCompV28.txt.gz
    2. Uncompress the file. 
      gunzip wgEncodeGencodeCompV28.txt.gz
    3. Isolate columns 2 till the end, removing the bin column, and saving as wgCompV28Cut.txt. 
      cut -f 2- wgEncodeGencodeCompV28.txt > wgCompV28Cut.txt
    4. Convert the genePred extended file to a bigGenePred text file, reordering and adding columns. 
      genePredToBigGenePred wgCompV28Cut.txt wgEncodeGencodeCompV28BigGP.txt
    5. Obtain input files for the binary conversion. 
      fetchChromSizes hg38 > hg38.chrom.sizes
 wget https://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigGenePred.as