how to report only 1 hit read by bowtie2?

[zhouzaiwei]

in bowtie1 there is a parameter -m 1 to report only 1 hit read, how to do this in bowtie2?

[a_mt]

In bowtie2 if a read aligns to multiple locations it has XS tag. You can simply use sed to delete lines with this tag, if this is what you wanted.

[zhouzaiwei]

thanks a lot, this is what i wanted.