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?
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?
