I met an issue when I aligned PE reads to homo genome sequence with bowtie2.
When I decreased the acceptable score to L,-1,-1, the alignment was successful with some tags such as "64M1D86M ... AS:i:-8 XS:i:-13 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:64^A86 YS:i:-8 YT:Z:CP" , the AS value is -8 which is not too low, howerver, the alignment was failure with L,-0.6,-0.6(default). does the issue releate to deletion? I can't figure it out, would you kindly to help me.
Dear doctor,
I met an issue when I aligned PE reads to homo genome sequence with bowtie2. When I decreased the acceptable score to L,-1,-1, the alignment was successful with some tags such as "64M1D86M ... AS:i:-8 XS:i:-13 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:64^A86 YS:i:-8 YT:Z:CP" , the AS value is -8 which is not too low, howerver, the alignment was failure with L,-0.6,-0.6(default). does the issue releate to deletion? I can't figure it out, would you kindly to help me.
thanks a lot.