Tophat Singletons And Problems For Converting From Bam To Fastq

Question

[bob-lowlow]

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?