Extract unique reads from SAM file

Question

[niu.shengyong]

I'm now trying to develop some packages written in R. I've conducted mapping through Rsubread and produce SAM file by the function of asSam in Rsamtools. However, I don't know how to extract the unique mapping reads in the SAM file. In the previous approach, I know people would extract the unique reads by the tag of XT:A:U, but I don't have the tag in the current version of SAM. Any suggestion? Thanks!

Simon

[cschu181]

Here are some thoughts: BWA mem how to know if a read is mapped uniquely?