added exclusion range to cross-correlation

dunnart/Snakefile

@@ -460,11 +460,14 @@ rule subsample_aligned_reads:
         shell("zcat {input} > {output.tmp}")
 
 # Determine exclusion range for fragment length estimation.
+## From bamPEFragmentSize (deepTools) average fragment length is ~220bp
+## See bamPEFragmentSize.histogram.png
 # Use a fixed lowerbound at -500.
-# Upperbound EXCLUSION_RANGE_MAX is
+# Upperbound E
+#EXCLUSION_RANGE_MAX is
 #   Histone ChIP-seq:  max(read_len + 10, 100)
 # lowerbound is fixed at 500 for both
-# read length is 50 because that is what we trimmed it to??
+
 
 rule cross_correlation_SSP:
     input: