Hi everyone,
I would like to obtain some kind of metric that represents how uniquely a sequence maps to the genome. Similar, in principle, to PeakSeq's mappability index.
MAPQ scores seem to be a good place to start. But, can anyone say how the p-values are calculated in Bowtie2?
There is a similar thread in SeqAnswers for Bowtie -- http://seqanswers.com/forums/showthr...highlight=mapq -- but, I am unsure whether it is accurate, and I don't know if Bowtie2 continues with that method.
Thanks for any help.
I would like to obtain some kind of metric that represents how uniquely a sequence maps to the genome. Similar, in principle, to PeakSeq's mappability index.
MAPQ scores seem to be a good place to start. But, can anyone say how the p-values are calculated in Bowtie2?
There is a similar thread in SeqAnswers for Bowtie -- http://seqanswers.com/forums/showthr...highlight=mapq -- but, I am unsure whether it is accurate, and I don't know if Bowtie2 continues with that method.
Thanks for any help.
