diff repmatch_gff3.xml @ 12:34d134cd4ca9 draft

Uploaded

--- a/repmatch_gff3.xml	Wed Dec 02 20:32:21 2015 -0500
+++ b/repmatch_gff3.xml	Wed Dec 16 14:45:32 2015 -0500
@@ -95,20 +95,37 @@
     <help>
 **What it does**
 
-Replicate matching - inspects paired peaks from two or more replicates and produces a list of matched
-paired peaks and optionally a list of unmatched paired peaks.  Additional optional outputs include the
-median read count for each input, details and a histogram.
+RepMatch accepts two or more input datasets, and starts by defining peak-pair midpoints in the first dataset.  It then
+discovers all peak-pair midpoints in the second dataset that are within the distance, defined by the tool's **Maximum
+distance between peaks in different replicates to allow merging** parameter, from the peak-pair midpoint coordinate in
+the first dataset.  When encountering multiple candidates to match (one-to-many), RepMatch uses the method defined by
+the tool's **Method of finding match** parameter so that there is at most only a one-to-one match across the two datasets.
+This method provides the following options:
+
+ * **closest** - matches only the closest one in bp distance.
+ * **largest** -  matches the one that contain the most number of reads.
+ * **all** -  both methods are run separately.
+
+RepMatch matching is an iterative process, as it attempts to find the centroid coordinate amongst all replicates. As such,
+the centroid is the point of reference for "distqnce" and "closest".  This process can be sped up by increasing the tool's
+**Step size** parameter.
+
+The minimum number of replicates that can be matched for a match to occur is defined by the tool's **Minimum number of
+replicates that must be matched for merging to occur** parameter.  Additional filters can be applied using the tool's
+**Advanced options**, including a lower and upper limit for the C-W distance.
+
+.. image:: $PATH_TO_IMAGES/repmatch.png
 
 -----
 
 **Options**
 
-* **Distance** - Maximum distance between peaks in different replicates to allow merging.
-* **Method** - Method to use when calling replicates.
-* **Step Size** - Distance for each iteration.
-* **Replicates** - Minimum number of replicates to call a peak.  Number of replicates required must be at least 2.
-* **Lower Limit** - Lower limit for the Crick-Watson distance filter.
-* **Upper Limit** - Upper limit for the Crick-Watson distance filter.
+ * **Distance** - Maximum distance for discovering all peak-pair midpoints in a second dataset relative to the peak-pair midpoints in the first dataset
+ * **Method** - Method to use when encountering multiple candidates to match so that there is at most only a one-to-one match across the two datasets.
+ * **Step Size** - Distance for each iteration.
+ * **Replicates** - Minimum number of replicates that can be matched for a match to occur.  This value must be at least 2.
+ * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
+ * **Upper Limit** - Upper limit for the Crick-Watson distance filter.
 
     </help>
     <expand macro="citations" />