Hi everyone!,
After running “Align reads and estimate abundance on a de novo assembly of RNA-Seq data”, I’m trying to run “Build expression matrix for a de novo assembly of RNA-Seq data by Trinity”. One consideration is that, in order to run Trinity assembly and Align reads and estimate abundance, I first concatenated samples (there are so many samples), so I have 2 samples (forward and reverse). I obtained 2 files when I run Align and estimate abundance: gene counts and isoform counts. In order to run Build expression matrix I’m not sure which samples I should use: I would use “gene counts” in Abundance estimates, and Gene to transcripts map (from Trinity) in Gene to transcript correspondence (‘gene(tab)transcript’ lines). Is that correct?, thanks in advance!