DESeq2 on de novo reads

Question

[pthom010]

I have a series of de novo assembled reads from Trinity from an organism without an annotated genome. I was wondering if it was possible to use DESeq2 through R to do my diffrerential expression analysis. I quantified my gene/transcript counts using RSEM.

[Asaf]

Why not? DESeq2 can work with count table of everything.

Answer 1

[h.mon]

Wonder no more! Read the manual and dispel any doubts you may have:

Differential Expression Analysis Using a Trinity Assembly

Spoiler:

Trinity provides support for several differential expression analysis tools, currently including the following R packages:

edgeR : http://bioconductor.org/packages/release/bioc/html/edgeR.html

DESeq2: http://bioconductor.org/packages/release/bioc/html/DESeq2.html

limma/voom: http://bioconductor.org/packages/release/bioc/html/limma.html

ROTS: http://www.btk.fi/research/research-groups/elo/software/rots/

[pthom010]

Thanks, but I wanted to do the DE analysis myself in R. I'm not able to customize Trinity's parameters to my liking but wasn't sure if I could upload my RSEM values into R.

[h.mon]

When you run Trinity wrapper scripts, it creates R scripts to run the differential expression analysis. You can then edit the scripts to your liking and run them.