bowtie 2 randomness

[carolW]

Hi,
Is it possible to have the same alignment for identical reads with bowtie 2 or should bowtie 1 be used? That is there are some genomic positions that should have the same number of mapped reads but they output different number of reads. Does it come from the alignment randomness and how to switch it off?

Thanks

Carol

[TiborNagy]

Bowtie use a pseudo random generator. If you use the --seed option with the same parameter, Bowtie will use the same "random" numbers during the process.