5be46d85fff4ff69ed2faae7e7c5ed0c3ddbe51b
markd
  Thu Jan 13 10:23:43 2011 -0800
clarified doc
diff --git src/hg/genePredToGtf/genePredToGtf.c src/hg/genePredToGtf/genePredToGtf.c
index bdf5aca..16dd84f 100644
--- src/hg/genePredToGtf/genePredToGtf.c
+++ src/hg/genePredToGtf/genePredToGtf.c
@@ -14,31 +14,34 @@
 /* Explain usage and exit. */
 {
 errAbort(
   "genePredToGtf - Convert genePred table or file to gtf.\n"
   "usage:\n"
   "   genePredToGtf database genePredTable output.gtf\n"
   "If database is 'file' then track is interpreted as a file\n"
   "rather than a table in database.\n"
   "options:\n"
   "   -utr - Add 5UTR and 3UTR features\n"
   "   -honorCdsStat - use cdsStartStat/cdsEndStat when defining start/end\n"
   "    codon records\n"
   "   -source=src set source name to uses\n"
   "   -addComments - Add comments before each set of transcript records.\n"
   "    allows for easier visual inspection\n"
-  "Note: use refFlat or extended genePred table to include geneName\n"
+  "Note: use refFlat (tables only) or extended genePred file/table to include\n"
+  "geneName.  If you are using genePred with starts with a numeric bin number,\n"
+  "drop it using the UNIX cut command:\n"
+  "    cut -f 2- in.gp |  genePredToGtf file stdin out.gp\n"
   );
 }
 
 /* FIXME:
  *   - right now, if not using -honorCdsStat and the CDS is not a multiple of
  *     three, a start_codon is written but not a stop_codon.  This is
  *     deceptive.  Should really not output either, maybe add a comment.
  */
 
 static struct optionSpec options[] = {
    {"utr", OPTION_BOOLEAN},
    {"honorCdsStat", OPTION_BOOLEAN},
    {"source", OPTION_STRING},
    {"addComments", OPTION_BOOLEAN},
    {NULL, 0}