q_value in cuffdiff results
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3.1 years ago
wangdp123 ▴ 250

Hello,

Does anyone notice that when running twice cuffdiff software for the same dataset, the resultant q_value could be slightly different (not exactly the same)?

Is this normal? Why could this happen?

Many thanks,

Tom

RNA-Seq Cuffdiff • 683 views
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I don't know the internals of cuffdiff, but the fact it has a --seed parameter strongly suggests it is non-deterministic. Set the seed and then check if results are identical.

--seed value of random number generator seed [ default: 0 ]

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