Dear all,
I am using Bowtie2.1.0 to analyze the reads from Illumina machines. The parameter I used are --end-to-end -D 5 -R 1 -N 0 -L 22 -i S,0,2.50.
One of my reads is TTAAAGGAACCCAGAGAGATATTTCA, and Bowtie gave me
HWI-ST1225 0 chr2 227981508 24 26M * 0 0 TTAAAGGAACCCAGAGAGATATTTCA BBBFFFFFFFFFFIIFFFIIIIIFII AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:12T13 YT:Z:UU
Since I set max number of mismatches in seed alignment as 0 (-N 0) and length of seed is 22 (-L 22), I didn’t expect any mismatch within 22 bases. However, Bowtie gave me 12T13. Did I misinterpreted the Bowtie options?
Thank you so much.
I am using Bowtie2.1.0 to analyze the reads from Illumina machines. The parameter I used are --end-to-end -D 5 -R 1 -N 0 -L 22 -i S,0,2.50.
One of my reads is TTAAAGGAACCCAGAGAGATATTTCA, and Bowtie gave me
HWI-ST1225 0 chr2 227981508 24 26M * 0 0 TTAAAGGAACCCAGAGAGATATTTCA BBBFFFFFFFFFFIIFFFIIIIIFII AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:12T13 YT:Z:UU
Since I set max number of mismatches in seed alignment as 0 (-N 0) and length of seed is 22 (-L 22), I didn’t expect any mismatch within 22 bases. However, Bowtie gave me 12T13. Did I misinterpreted the Bowtie options?
Thank you so much.
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