I am about to do some RNA-seq analysis to find differently expressed (DE) genes between different conditions. I am studying a nematode which is relatively unknown but for which I have a genome assembled (not published yet).
Now because I have a genome I could use the tuxedo pipeline (tophat / Cufflinks / Cuffdiff) to find the DE genes. But my concern is that the genome is newly assembled and therefore not very polished. I also read this post (Is There Any Reason To Do De Novo Transcript Assembly If A Reference Is Available?) which made me think that perhaps using both the de novo and the genome-guided strategies was better.
I then found that is it possible to combine de novo transcriptome assemblies with genome-guided assemblies (http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2277-7 , http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091776) by using the tr2aacds pipeline of EvidentialGene (http://arthropods.eugenes.org/genes2/about/EvidentialGene_trassembly_pipe.html).
If I'm understanding correctly, I would then have (I hope) a very good transcriptome to which I could align my reads (both conditions separately) and perform the differential expression analysis.
My question is: is it a good ideia / justified to do the RNA-seq analysis using a transcriptome assembled de novo as well as genome-guided? Or is the tuxedo pipeline better?
Advices very much appreciated!
Best Wishes, Sophie