Question: Extract aligned exactly 1 time fron Bowtie2?
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I have an output from Bowtie2 aligner as below:
16075710 reads; of these:
16075710 (100.00%) were unpaired; of these:
375049 (2.33%) aligned 0 times
11575941 (72.01%) aligned exactly 1 time
4124720 (25.66%) aligned >1 times
97.67% overall alignment rate
I like to extract unique aligns from that results, I also use below command but they do not give me correct number of unique aligns.
samtools view -Sh data.sam | grep -e "^@" -e "XM:i:[0][^0-9]" | grep -v "XS:i:" | wc -l
4811303
samtools view -hf 0x2 data.sam | grep -v "XS:i:" | wc -l
430
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modified 6 months ago
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Jennifer Hillman Jackson ♦ 25k
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6 months ago by
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