Question: DESeq2 and DEXSeq
gravatar for pthom010
3 months ago by
pthom0100 wrote:

I have reads from 30 samples that I de novo assembled with Trinity and started using the assembly in a differential expression analysis in DESeq2. However, I also have supertranscripts assembled by Trinity and recently learned about DEXSeq. Would it be redundant to finish my DESeq analysis and then do the DEXSeq analysis and compare the results? Or is there a way to incorporate my gff file into DESeq that would still provide a valid analysis?

deseq2 trinity dexseq • 159 views
ADD COMMENTlink written 3 months ago by pthom0100

DESeq2 is for differential gene expression and DEXSeq is for differential exon usage. Both are different things. What is your aim here?

ADD REPLYlink written 3 months ago by ashish570

Essentially, I have two unique individuals we did a time course on and I wanted to look at differential exon usage and gene expression. So I want to do both things but was wondering if there was a program that could incorporate my DESeq and DEXSeq data to enhance my analysis.

ADD REPLYlink written 3 months ago by pthom0100

There are no programs which can incorporate both deseq and dexseq according to my knowledge. However, if you are interested in splicing I would suggest junctionseq instead of dexseq.

ADD REPLYlink written 3 months ago by ashish570
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