Is it ok to implement Cufflinks/Cuffdiff with the STAR aligned files for the differential gene expression analysis?

Question

[Meeran]

Hi,

I have the RNA-Seq data of potato (Solanum tuberosum) with two conditions and I am planing to perform the differential gene expression analysis. I know Tophat and Cufflinks are the well established pipeline but I wish to switch to STAR for the alignment purpose. I would like to know if it is ok to implement STAR and Cufflinks in the same pipeline?

Thanks

Answer 1

[ATpoint]

I know Tophat and Cufflinks are the well established pipeline

Yes, back in the early 2010s, that is over a decade ago and both tools are considered deprecated by now, having more elaborate successors. You can use STAR indeed, it's a great tool, and downstream of that you could use something like featureCounts to make a count matrix and then analyse for differential expression with DESeq2, edgeR or limma-voom. Don't use cufflinks, its normalization is by todays standards suboptimal and there is simply no reason to use it anymore.