We have SE 100bp reads aligned with bowtie2. We noticed that when keep other options the same, but change -N 0 to -N 1, we got some really different alignments, see example below:
Output:
Output:
I'm confused about the results. I thought -N 1 should be able to pick up the best alignment with -N 0, how come the alignment results are so much worse when -N 1 for the same read?
Thanks in advance!
Code:
bowtie2 -x ./hg19/hg19_all --end-to-end -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 --score-min L,-1,-1 -c AGAGCTGTTCCTATTCGGCCATCTTGGCTCCTCCTCCCGGATTCACTGATTTTTTGAAGGGTTTTTTGTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTT
Code:
0 0 chr4 58434477 42 101M * 0 0 AGAGCTGTTCCTATTCGGCCATCTTGGCTCCTCCTCCCGGATTCACTGATTTTTTGAAGGGTTTTTTGTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:0G72T27 YT:Z:UU
Code:
bowtie2 -x ./hg19/hg19_all --end-to-end -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --score-min L,-1,-1 -c AGAGCTGTTCCTATTCGGCCATCTTGGCTCCTCCTCCCGGATTCACTGATTTTTTGAAGGGTTTTTTGTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTT
Code:
0 16 chr2 136138378 0 60M5I1M1I34M * 0 0 AAGATCAGAGCAGAACTGAAGGAGATAGAGACACAAAAAACCCTTCAAAAAATCAGTGAATCCGGGAGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-88 XN:i:0 XM:i:10 XO:i:2 XG:i:6 NM:i:16 MD:Z:13C11C3A8C18T5C2T0T11A14C0 YT:Z:UU
Thanks in advance!