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

diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html
index 8cb7874..f2c1fe3 100755
--- src/hg/htdocs/FAQ/FAQformat.html
+++ src/hg/htdocs/FAQ/FAQformat.html
@@ -1110,30 +1110,32 @@
     char[1] strand;     	"+ or - for strand"
     uint txStart;       	"Transcription start position"
     uint txEnd;         	"Transcription end position"
     uint cdsStart;      	"Coding region start"
     uint cdsEnd;        	"Coding region end"
     uint exonCount;     	"Number of exons"
     uint[exonCount] exonStarts; "Exon start positions"
     uint[exonCount] exonEnds;   "Exon end positions"
     int score;            	"Score"
     string name2;       	"Alternate name (e.g. gene_id from GTF)"
     string cdsStartStat; 	"Status of CDS start annotation (none, unknown, incomplete, or complete)"
     string cdsEndStat;   	"Status of CDS end annotation (none, unknown, incomplete, or complete)"
     lstring exonFrames; 	"Exon frame offsets {0,1,2}"
     )
 </code></pre>
+<p>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>
 
 <a name=RefFlat></a>
 <p><strong>Gene Predictions and RefSeq Genes with Gene Names</strong></p>
 <p>
 A version of genePred that associates the gene name with the gene prediction information. In 
 alternative-splicing situations, each transcript has a row in this table.</p>
 <pre><code>table refFlat
 "A gene prediction with additional geneName field."
     (
     string  geneName;           "Name of gene as it appears in Genome Browser."
     string  name;               "Name of gene"
     string  chrom;              "Chromosome name"
     char[1] strand;             "+ or - for strand"
     uint    txStart;            "Transcription start position"
     uint    txEnd;              "Transcription end position"