f91588820743d9970f0700b44cba9fbecac98bf3
max
  Wed Aug 14 09:26:32 2024 -0700
changing text after feedback from QA, refs #34268

diff --git src/hg/hgTables/intersect.c src/hg/hgTables/intersect.c
index 2c425a2..c969e4f 100644
--- src/hg/hgTables/intersect.c
+++ src/hg/hgTables/intersect.c
@@ -268,30 +268,38 @@
     }
 else
     {
     /*	keep javaScript onClick happy	*/
     jsTrackingVar("op", op);
     
     jsInline
 	(
 	"var invertTable=0;\n"
 	"var invertTable2=0;\n"
     	);
 
     hPrintf("(data track %s is not composed of gene records.  Specialized intersection operations are not available.)<P>\n", name);
     }
 
+char *hgsid = cartSessionId(cart);
+hPrintf("<P style='margin-top:3px; margin-bottom:10px; padding:0px'>");
+hPrintf("<b>If these options are not sufficient:</b><BR>The intersection configured on this page only outputs fields from the track selected under \"Select Dataset\" on the previous page, for those features that are overlapped by the second track, selected on this page.<BR>");
+hPrintf("If you want to intersect two tracks and output fields from both, e.g. to show which Chip-seq peak overlaps which enhancer, or which dbSNP variant overlaps which ClinVar CNV, then use our <a href='hgIntegrator?hgsid=%s'>Data Integrator</a>.<BR>", hgsid);
+hPrintf("If you want to annotate a track with variants in VCF format with the transcript positions, then use our <a href='hgVai?hgsid=%s'>Variant Annotation Integrator</a>.<br>", hgsid);
+hPrintf("More complex operations may require command line tools. We provide <a target=_blank href='https://hgdownload.soe.ucsc.edu/admin/exe/'>several hundred command line tools</a> that can help with overlaps and intersections, e.g. overlapSelect, featureBits, pslMap and others.<br>");
+hPrintf("</P>");
+
 cgiMakeButton(hgtaDoIntersectSubmit, "Submit");
 hPrintf(" ");
 cgiMakeButton(hgtaDoMainPage, "Cancel");
 hPrintf("</FORM>\n");
 
 /* Hidden form - for benefit of javascript. */
     {
     static char *saveVars[32];
     int varCount = ArraySize(nextVars);
     memcpy(saveVars, nextVars, varCount * sizeof(saveVars[0]));
     saveVars[varCount] = hgtaDoIntersectMore;
     jsCreateHiddenForm(cart, getScriptName(), saveVars, varCount+1);
     }
 
 htmlClose();