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-   -   removing singletons from tophat output (http://seqanswers.com/forums/showthread.php?t=26709)

Derek-C 01-21-2013 02:18 AM

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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