28aa0d3b6f9ec11895b49f1eb8117d868393fa42
lrnassar
  Tue Oct 15 05:21:23 2024 -0700
Updating the description of the exon frame field, refs #32675

diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html
index afcf5aa..98a6290 100755
--- src/hg/htdocs/goldenPath/help/bigGenePred.html
+++ src/hg/htdocs/goldenPath/help/bigGenePred.html
@@ -42,45 +42,47 @@
     string chrom;       	"Reference sequence chromosome or scaffold"
     uint   chromStart;  	"Start position in chromosome" 
     uint   chromEnd;    	"End position in chromosome"
     string name;        	"Name or ID of item, ideally both human-readable and unique"
     uint score;         	"Score (0-1000)"
     char[1] strand;     	"+ or - for strand"
     uint thickStart;    	"Start of where display should be thick (start codon)"
     uint thickEnd;      	"End of where display should be thick (stop codon)"
     uint reserved;       	"RGB value (use R,G,B string in input file)"
     int blockCount;     	"Number of blocks"
     int[blockCount] blockSizes; "Comma separated list of block sizes"
     int[blockCount] chromStarts;"Start positions relative to chromStart"
     string name2;       	"Alternative/human readable name"
     string cdsStartStat; 	"Status of CDS start annotation (none, unknown, incomplete, or complete)"
     string cdsEndStat;   	"Status of CDS end annotation (none, unknown, incomplete, or complete)"
-    int[blockCount] exonFrames; "Exon frame {0,1,2}, or -1 if no frame for exon"
+    int[blockCount] exonFrames; "Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region."
     string type;        	"Transcript type"
     string geneName;    	"Primary identifier for gene"
     string geneName2;   	"Alternative/human-readable gene name"
     string geneType;    	"Gene type"
     )  </code></pre>
 
-<p>The field <pre>exonFrames</pre> is a comma-separated list of the numbers 0, 1, 2 or -1, one per exon, in order of transcription.
-This order means that the first value for a transcript on the - strand is the exon most on the right of the screen 
-on the Genome Browser. A value of zero means that the first codon of the exon starts at the first nucleotide of the
-exon. A value of one means that the first codon starts after the first nucleotide and a value of two means
-that it starts after the second nucleotide. UTRs are non-coding and their exonFrame value is -1.
-</p>
+<p>
+The field <code>exonFrames</code> is a comma-separated list of the numbers
+with the possible values 0, 1, 2 or -1, one per exon, in order of transcription.
+This order means that the first value for a transcript on the minus (-) strand is
+the exon on the right of the screen on the Genome Browser.
+A value of zero means that the first codon of the exon starts at the first nucleotide of the
+exon. A value of one means that the first codon starts after the first
+nucleotide and a value of two means that it starts after the second nucleotide.
+UTRs are non-coding and their exonFrame value is -1.</p>
 
-values indicate the offset of the first codon in nucleotides at the start of the exon. 
 <p>The fields cdsStartStat and cdsEndStat have the following values: 'none' = none,
 'unk' = unknown, 'incmpl' = incomplete, and 'cmpl' = complete. The
 values, however, are not used for our display and cannot be used to identify coding or non-coding genes.
 For most purposes, to get more information about a transcript, other tables will need to be used. For
 instance, in the case of hg38, the tables named wgEncodeGencodeAttrsVxx, where xx is the Gencode Version number.
 See this <a href="../../FAQ/FAQgenes.html#coding" target="_blank">coding/non-coding genes FAQ</a>
 for more information.</p>
 <p>
 The following bed12+8 is an example of a <a href="examples/bigGenePred.txt">pre-bigGenePred text file
 </a>.</p>
 
 <h2>Creating a bigGenePred track from a bed12+8 file</h2>
 <p>
 <strong>Step 1.</strong> 
 Format your pre-bigGenePred file. The first 12 fields of pre-bigGenePred files are described by the