Using Trinity for DGE - how to input study design

Question

[hydra_questions]

I'm using trinity to perform a denovo transcriptome assembly to identify deferentially expressed genes between different treatment AND cut types (different sites of injury). I was wondering if there was a way to input the design so the expression levels are compared to the respective controls

Alternatively, I've been trying to export the gene count matrix produced by trinity so I could conduct the analysis in R instead of command line but have been unsuccessful. I'm not sure if there is a way to do this maybe?

Thanks in advance!

[h.mon]

Trinity provides wrapper scripts to automate DGE analysis, see Differential Expression Analysis Using a Trinity Assembly. The wrapper scripts will create the R code on the fly, you can then open this code and modify the DGE analysis scripts to suit your needs.

[Ram]

Trinity does de novo RNAseq assembly. I don't think you can do DE analysis with Trinity. How are you getting the gene expression results from Trinity-assembled data? Are there de novo DE tools out there?

[geneticatt]

I guess that your controls will be a non-injured specimens from different treatments. This question doesn't seem very relevant to the Trinity de-novo assembler, instead this inform the strategy of downstream analysis and potentially the construction of a combined reference which is built from the libraries of all (or a subset) of samples. Do you have multiple phenotypes involved or are all specimens clonal?

Once you reach the step of performing DE analyses (after assembly/filtering/mapping/expr_estimates) you can perform a multivariate DE analysis. This is an option for DESeq2 and likely other packages.