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Old 04-03-2015, 01:03 AM   #63
joshquick
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Location: Birmingham

Join Date: Jul 2012
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When you decreased the SPRI ratio you increased the insert size and we found bowtie2 behaves weirdly above 500bp inserts with the default settings. You might want to change your bowtie2 settings or try bwa-mem:

http://nickloman.github.io/2013/05/0...era-libraries/
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