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Biscuit: Is alignment stochastic?

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?

alignment biscuit

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1 answer

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

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