547d66239f70b9636b33694ec29a8042e66e95aa
max
  Thu Mar 3 08:19:38 2022 -0800
adding cdsStartStat docs, refs #29030

diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html
index 1f92ddd..085f78f 100755
--- src/hg/htdocs/goldenPath/help/bigGenePred.html
+++ src/hg/htdocs/goldenPath/help/bigGenePred.html
@@ -46,30 +46,33 @@
     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"
     string type;        	"Transcript type"
     string geneName;    	"Primary identifier for gene"
     string geneName2;   	"Alternative/human-readable gene name"
     string geneType;    	"Gene type"
     )  </code></pre>
 
+<p><b>cdsStartStat/cdsEndStat</b>: If you want only protein-coding transcripts, then filter for cdsStartStat='cmpl' and cdsEndStat='cmpl'. Non-coding transcripts have either one of these set to 'incmpl'.
+</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
 <a href="../../FAQ/FAQformat.html#format1">BED file format</a>. Your file must
 also contain the 8 extra fields described in the autoSql file definition 
 shown above: <code>name2, cdsStartStat, cdsEndStat, exonFrames, type, geneName, geneName2, 
 geneType</code>. For example, you can use this bed12+8 input file, 
 <a href="examples/bigGenePred.txt">bigGenePred.txt</a>. Your pre-bigGenePred file must be sorted 
 first on the <code>chrom</code> field, and secondarily on the <code>chromStart</code> field. You
 can use the UNIX <code>sort</code> command to do this:</p>