Optimal params for Bowtie

[JohnK]

Hi, I'm hoping this isn't a re-post (maybe I didn't search the right keywords), but I'm looking for optimal parameters for some Illumina paired-end data I'd like to map via Bowtie. Does anyone have any suggestions? Thank you for your help!

J

[csoong]

unfortunately John, there is no optimal parameters it all depends on what you're looking for. it may sound crazy -- good luck!