shrink log fold change option in Trinity pipeline?

[Holly Williams]

Hi, am I correct that DESeq2 is used in Trinity's run_DE_analysis.pl step?  I understand that only older versions of DESeq2 performed shrinkage of LFC (log fold change) estimates by default, but the newer versons do not.  I am planning to run a GSEA, where shrunken values should be provided. Is there a way to include a log fold change option in the run_DE_analysis.pl step?  Thank you!

Here is the information I found about log fold change shrinkage in DESeq2:

Gene-level differential expression analysis with DESeq2 | Introduction to DGE - ARCHIVED (hbctraining.github.io)

Sincerely,

Holly Williams

[Brian Haas]

Hi,

The trinity script doesn't run shrinkage of LFC if it's not part of the default installation of DESeq2.  But, Trinity generates an R script that it then executes to run the DESeq2 analysis. You can modify that R script to include any additional functionality such as the LFC shrinkage step.  

hope this helps