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Old 01-21-2013, 01:18 AM   #1
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Location: U.S.A.

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Default removing singletons from tophat output

Hi all,

I'm trying to get my tophat output without singletons (I'm trying to convert the output back into fastq format so everything needs a mate) but even with both the no-mixed and no-discordant options in tophat, samtools flagstat is still identifying millions of singletons, which are then essentially discarded when converting to fastq. Any ideas?
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