From 77cc4eff55d816ac9f5980461d0a0844a1d47eaa Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 7 Aug 2020 19:57:21 +1000
Subject: [PATCH] added exclusion range to cross-correlation

---
 dunnart/Snakefile | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/dunnart/Snakefile b/dunnart/Snakefile
index 0ae59b3..1abbeb8 100644
--- a/dunnart/Snakefile
+++ b/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:
-- 
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