I used BWA before,after mapping to genome or cDNA,I can filter unique mapping reads by sam flag value,but BWA mapping efficiency is not as good as bowtie2,so now I use bowtie2 instead.But I don't know the bowtie2 flag value that can indicate unique mapping.Could I get some answers?Thank you.
If you are running bowtie2 with the -k or -a options, then any read that has only a single output alignment can be considered uniquely mapped. If you're using the default reporting only the best alignment, the you should set a threshold on the MAPQ score reported based on how uniquely mapping you required your alignment.
Among the optional fields reported by bowtie2 you have :
XS:i:<n> aln score for next best aln (only reported if >1 aln found)
So the absence of this field for a read (in addition to the mapping flag and MAPQ) can be a sign of uniqueness ?