Bowtie2 parameters for a more stringent mapping

[ysb]

Hi all,

I'm using bowtie2 with the default settings to map SE 50bp Chip-seq reads against a bovine genome. I'm getting too many overall reads aligned and too many reads aligned >1 times:

21041950 reads; of these:
21041950 (100.00%) were unpaired; of these:
750299 (3.57%) aligned 0 times
10685944 (50.78%) aligned exactly 1 time
9605707 (45.65%) aligned >1 times
96.43% overall alignment rate

I was wondering if any of you have had this issue and/or know which parameters I need to change to get a more stringent mapping.

Thanks a lot,

-Yanina