From cb1ef93e42e9e95718a8be5a42b2a182aece0648 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 11 Dec 2020 12:27:56 +1100
Subject: [PATCH] added chainCleaner

---
 cross_species_comparison/README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/cross_species_comparison/README.md b/cross_species_comparison/README.md
index 31d70ab..1b63dab 100644
--- a/cross_species_comparison/README.md
+++ b/cross_species_comparison/README.md
@@ -214,7 +214,6 @@ chainCleaner improves the specificity in genome alignment chains by detecting an
 
 ```
 chainCleaner smiCra1_mm10_repFil.chain mm10.2bit smiCra1.2bit smiCra1_mm10_repFill_chainCl.chain smiCra1_mm10_repFill_chainCl.bed -tSizes=mm10.chrom.sizes -qSizes=smiCra1.chrom.sizes -LRfoldThreshold=2.5 -doPairs -LRfoldThresholdPairs=10 -maxPairDistance=10000 -maxSuspectScore=100000 -minBrokenChainScore=75000 -linearGap=loose
-
 ```
 
 `-LRfoldThreshold` = threshold for removing local alignment blocks if the score of the left and right fill of brokenChain. Default is 2.5
-- 
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