Biscuit: Is alignment stochastic?

Question

[irfanwustl]

I have WGBS pair-end fastq files. I am using Biscuit aligner. Is alignment stochastic? Can we get (slightly) different alignment from different runs on the same fastq files?

[WouterDeCoster]

Changed your title to make it more specific, and added biscuit tag. Please think about this in the future, as such experts can more easily find your question.

Answer 1

[zwdzwd]

No, the mapping shouldn't be stochastic. There might be some deterministic arbtrariness for choosing among equal optimalities.