--- a/genetrack.xml	Wed Dec 16 14:17:15 2015 -0500
+++ b/genetrack.xml	Wed Dec 16 19:53:24 2015 -0500
@@ -137,6 +137,44 @@
  * **Exclusion zone of upstream called peaks** - Defines the exclusion zone centered over peaks upstream of a peak.
  * **Exclusion zone of downstream called peaks** - Defines the exclusion zone centered over peaks downstream of a peak.
  * **Filter** - Absolute read filter, restricts output to only peaks with larger peak height.
+ 
+ -----
+
+**Output gff Columns**
+
+ 1. Chromosome
+ 2. Script
+ 3. Placeholder (no meaning)
+ 4. Start of peak exclusion zone (-e 20)
+ 5. End of peak exclusion zone
+ 6. Tag sum (not peak height or area under curve, which LionDB provides)
+ 7. Strand
+ 8. Placeholder (no meaning)
+ 9. Attributes (standard deviation of reads located within exclusion zone) = fuzziness of peak
+
+ -----
+ 
+ **Considerations**
+ 
+ In principle, the width of the exclusion zone may be as large as the DNA region occupied by the native protein
+ plus a steric exclusion zone between the protein and the exonuclease.  On the other hand the site might be considerably
+ smaller if the protein is in a denatured state during exonuclease digestion (since it is pre-treated with SDS).
+ 
+ In general, higher resolution data or smaller binding site size data should use smaller sigma values.  Large binding site
+ size data such as 147 bp nucleosomal DNA use a larger sigma value like 20 (-s 20).  For transcription factors mapped by
+ ChIP-exo, sigma may initially be set at 5, and the exclusion zone set at 20 (-s 5 –e 20).  Sigma is typically varied
+ between ~3 and ~20.  Too high of a sigma value may merge two independent nearby binding events.  This may be desirable if
+ closely bound factors are not distinguishable.  Too low of a sigma value will cause some tags that contribute to a binding
+ event to be excluded, because they may not be located sufficiently close to the main peak.  If alternative (mutually
+ exclusive) binding is expected for two overlapping sites, and these sites are to be independently recorded, then an
+ empirically determined smaller exclusion zone width is set.  Thus, the value of sigma is set empirically for each mapped
+ factor depending upon the resolution and binding site size of the binding event.
+
+It might make sense to exclude peaks that have only a single tag, where -F 1 is used, or have their tags located on only
+a single coordinate (called Singletons, where stddev=0 in the output file).  However, low coverage datasets might be
+improved by including them, if additional analysis (e.g., motif discovery) validates them.  In addition, idealized action
+of the exonuclease in ChIP-exo might place all tags for a peak on a single coordinate.
+
     </help>
     <expand macro="citations" />
 </tool>