# HG changeset patch
# User greg
# Date 1450316140 18000
# Node ID d31ef9abce7475998ee2e04eb817cdaddf124dd9
# Parent  34d134cd4ca9aad830ccacf6233788cbd3e89cf1
Uploaded

diff -r 34d134cd4ca9 -r d31ef9abce74 repmatch_gff3.xml
--- a/repmatch_gff3.xml	Wed Dec 16 14:45:32 2015 -0500
+++ b/repmatch_gff3.xml	Wed Dec 16 20:35:40 2015 -0500
@@ -127,6 +127,35 @@
  * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
  * **Upper Limit** - Upper limit for the Crick-Watson distance filter.
 
+-----
+
+**Output Data Files**
+
+ * **Data MP** - gff file consisting of only peak pairs
+
+  - Columns are **chr**, **script**, **blank**, **peak start**, **peak end**, **blank**, **normalized tag counts**, **blank** and **info**.
+  - Peak start and end are separated by one coordinate.
+  - Normalized tag is the occupancy averaged across replicates.
+  - Attributes include C-W distance, sum total of tag counts, number of replicates merged.
+
+ * **Data D** - tabular file consisting of the list of all matched replicates.
+ * **Data UP** - tabular file consisting of all unmatched peak-pairs.
+
+**Output Statistics Files**
+
+ * **Statistics Table** - tabular file providing the description key of **Data D**.
+ * **Statistics Histogram** - graph of the number of matched locations having the indicated replicate counts.
+
+**Comments on Replicates**
+
+Three types of replicates may be considered.  Biological replicates represent independently collected biological samples.
+At least two biological replicate must be performed for each experiment from which a conclusion is being drawn, and the
+conclusion must be evident in both biological replicates when analyzed separately.  Technical replicates represent a re-run
+of the assay on the same biological material.  This is usually done when one replicate fails to produce quality data, and is
+used to replace that earlier replicate.  Sequencing replicates represent additional sequencing of the same successful library
+in order to obtain more reads should the analysis require it.  The reads from individual sequencing replicates are usually
+merged without need for separate analysis.
+
     </help>
     <expand macro="citations" />
 </tool>