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Commit cb1ef93e authored by Laura Cook's avatar Laura Cook
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added chainCleaner

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cross_species_comparison/README.md
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......@@ -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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