Entering edit mode
4.1 years ago
pthom010
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40
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 is for differential gene expression and DEXSeq is for differential exon usage. Both are different things. What is your aim here?
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.
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.