Hi:
I recently compared the uniquely mapped reads generated with and without -g 1 option. However, I got very different answers.
with -g 1 option, the mapped reads were 9,737,100, about 68% of all reads.
without -g 1 option (default), the uniquely mapped reads were 12,440,838, about 87% of all reads.
The command used to check uniquely mapped reads is:
samtools view .bam | awk '$5==255{print $0}' | wc -l
Anyone knows why there is so large difference? Thanks.
Tao
I recently compared the uniquely mapped reads generated with and without -g 1 option. However, I got very different answers.
with -g 1 option, the mapped reads were 9,737,100, about 68% of all reads.
without -g 1 option (default), the uniquely mapped reads were 12,440,838, about 87% of all reads.
The command used to check uniquely mapped reads is:
samtools view .bam | awk '$5==255{print $0}' | wc -l
Anyone knows why there is so large difference? Thanks.
Tao