Off topic:bowtie2 unique align reads
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2.4 years ago
Ric ▴ 350

I ran bowtie2 in the following way:

bowtie2 -x tdna -U Sample-5-concat+trim-21.fq -S sample5.sam 
1792444 reads; of these:
  1792444 (100.00%) were unpaired; of these:
    1092638 (60.96%) aligned 0 times
    698850 (38.99%) aligned exactly 1 time
    956 (0.05%) aligned >1 times
39.04% overall alignment rate

How do I get reads which aligned exactly 1 time?

Thank you in advance.

alignment • 1.7k views
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