--- a/genetrack.xml	Wed Dec 16 19:59:14 2015 -0500
+++ b/genetrack.xml	Wed Dec 16 20:09:08 2015 -0500
@@ -138,37 +138,36 @@
  * **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**
 
- * Chromosome
- * Script
- * Placeholder (no meaning)
- * Start of peak exclusion zone (-e 20)
- * End of peak exclusion zone
- * Tag sum (not peak height or area under curve, which LionDB provides)
- * Strand
- * Placeholder (no meaning)
- * Attributes (standard deviation of reads located within exclusion zone) = fuzziness of peak
+ 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).
+**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.
+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 mappedfactor 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