I tried to get a uniquely mapped reads from BWA alignment, so I filtering out the alignments without XT:A:U in SAM line.
However, BWA produces odd aligned reads, which is both unmapped and uniquely mapped.
These reads below have both SAM flag which means 'reads unmapped' and mapping position.(chrom, pos)
How can that be? Have you ever gotten such reads?
SRR101341.21640516 4 chr3 199501827 0 33M * 0 0 GACCCTAACCCTAACCCTAACCCTAACCCTAAC 0)@@)?''0-68?09384;<5=)A;56@>167: XT:A:U NM:i:0 XN:i:1 X0:i:1 X1:i:557 XM:i:0 XO:i:0 XG:i:0 MD:Z:33
SRR101344.29575296 133 chr11 134452345 15 43M chr12 92723370 0 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGAGG CCCCCCCCCCCCCCCCCCDCCCCCDCCCCCBB@CCCBCCCC@C XT:A:U NM:i:0 XN:i:3 SM:i:15 AM:i:0 X0:i:1 X1:i:6 XM:i:0 XO:i:0 XG:i:0 MD:Z:43 XA:Z:chr3,+199385175,43M,1;chrX,+154913557,43M,1;chrY,+57772757,43M,1;chr11,+134452000,43M,1;chr1,-397,43M,1;chr18,-25,43M,1;
thanks (^______^)
However, BWA produces odd aligned reads, which is both unmapped and uniquely mapped.
These reads below have both SAM flag which means 'reads unmapped' and mapping position.(chrom, pos)
How can that be? Have you ever gotten such reads?
SRR101341.21640516 4 chr3 199501827 0 33M * 0 0 GACCCTAACCCTAACCCTAACCCTAACCCTAAC 0)@@)?''0-68?09384;<5=)A;56@>167: XT:A:U NM:i:0 XN:i:1 X0:i:1 X1:i:557 XM:i:0 XO:i:0 XG:i:0 MD:Z:33
SRR101344.29575296 133 chr11 134452345 15 43M chr12 92723370 0 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGAGG CCCCCCCCCCCCCCCCCCDCCCCCDCCCCCBB@CCCBCCCC@C XT:A:U NM:i:0 XN:i:3 SM:i:15 AM:i:0 X0:i:1 X1:i:6 XM:i:0 XO:i:0 XG:i:0 MD:Z:43 XA:Z:chr3,+199385175,43M,1;chrX,+154913557,43M,1;chrY,+57772757,43M,1;chr11,+134452000,43M,1;chr1,-397,43M,1;chr18,-25,43M,1;
thanks (^______^)
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