Question: Differetial analysis after HTSEq count
0
gravatar for rob.costa1234
2.6 years ago by
rob.costa1234160
United States
rob.costa1234160 wrote:

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 • 845 views
ADD COMMENTlink modified 2.6 years ago by Antonio R. Franco4.0k • written 2.6 years ago by rob.costa1234160

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

ADD REPLYlink written 2.6 years ago by vakul.mohanty240

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

ADD REPLYlink written 2.6 years ago by Chris Cole680
1
gravatar for Antonio R. Franco
2.6 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

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

ADD COMMENTlink written 2.6 years ago by Antonio R. Franco4.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1498 users visited in the last hour