I'm doing alignment with bwa (0.7.5a-r405).
But I found that the same sequence in different position may influence the mapping result.
As you may noticed, the read1 and read3 are exactly the same, but the mapping result is different.
read1 0 Chr3 209 0 50M * 0 0 CAAAGGTGCGGCCCGAGGTAAAGGGTTTAACGCTTCATATTTTATCACAT HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH XT:A:R NM:i:0 X0:i:2 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:50 XA:Z:Chr11,-26081473,50M,1;
read2 0 Chr3 208 0 50M * 0 0 ACAAAGGTGCGGCCCGAGGTAAAGGGTTTAACGCTTCATATTTTATCACA HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH XT:A:R NM:i:0 X0:i:2 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:50 XA:Z:Chr3,+4840,50M,0;Chr11,-26081474,50M,1;
read3 4 * 0 0 * * 0 0 CAAAGGTGCGGCCCGAGGTAAAGGGTTTAACGCTTCATATTTTATCACAT HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Does anyone know what's happening here?
the command line:
input=$1
bwa aln genome.fa $input >${input/.fq/}.sai
bwa samse -f ${input/.fq/}.sam genome.fa ${input/.fq/}.sai $input
But I found that the same sequence in different position may influence the mapping result.
As you may noticed, the read1 and read3 are exactly the same, but the mapping result is different.
read1 0 Chr3 209 0 50M * 0 0 CAAAGGTGCGGCCCGAGGTAAAGGGTTTAACGCTTCATATTTTATCACAT HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH XT:A:R NM:i:0 X0:i:2 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:50 XA:Z:Chr11,-26081473,50M,1;
read2 0 Chr3 208 0 50M * 0 0 ACAAAGGTGCGGCCCGAGGTAAAGGGTTTAACGCTTCATATTTTATCACA HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH XT:A:R NM:i:0 X0:i:2 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:50 XA:Z:Chr3,+4840,50M,0;Chr11,-26081474,50M,1;
read3 4 * 0 0 * * 0 0 CAAAGGTGCGGCCCGAGGTAAAGGGTTTAACGCTTCATATTTTATCACAT HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Does anyone know what's happening here?
the command line:
input=$1
bwa aln genome.fa $input >${input/.fq/}.sai
bwa samse -f ${input/.fq/}.sam genome.fa ${input/.fq/}.sai $input
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