Differetial analysis after HTSEq count

Question

[rob.costa1234]

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

[vakul.mohanty]

DEseq models the read count distribution and provides a robust comparison in comparison to a simple t-test or anova

[Chris Cole]

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

Answer 1

[Antonio R. Franco]

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