Differetial analysis after HTSEq count
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6.2 years ago
rob.costa1234 ▴ 310

What is the best tool/ software or method to perform a statistical analysis on HTseq count data . I s it simply performing aova or t tests or ay sophisticate methods like edgeR / DEseq which take raw reads?

Thanks

RNA-Seq • 1.7k views
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DEseq models the read count distribution and provides a robust comparison in comparison to a simple t-test or anova

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edgeR/DESeq/DESeq2/etc don't take raw reads. They take gene read counts from tools like HTseq-count or featureCounts.

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6.2 years ago

I would say that the reference methods for running DE analysis nowadays are those using DESeq2 /edgeR and the like because they assume a determined distribution of the data and use a linear model fit which are far more robust that a simple anova or t-test

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