hi
i have rum bowtie 2 using —very-sensitive option and got result like this
i just want to get the uniquely aligned reads alone i,e., 53.69% of reads (78126644). but my output file (sam format) seems to have the those which are aligned>1 times how to get rid of them?
in previous versions of bowtie i use to use -m option for that
i have rum bowtie 2 using —very-sensitive option and got result like this
Code:
14559177 reads; of these: 14559177 (100.00%) were unpaired; of these: 4317487 (29.65%) aligned 0 times 7816644 (53.69%) aligned exactly 1 time 2425046 (16.66%) aligned >1 times 70.35% overall alignment rate
in previous versions of bowtie i use to use -m option for that
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