I have to analyze RNA-Seq data from multiple species (human, bovine,...) and different cell types, to detect differentially expressed genes (DEGs) and to select common DEGs between species. I've two ideas in mind :
1. align each species to its related genome, and count the number of reads per gene using its related annotation (e.g. ENSEMBL). Then use DESeq2 to assess differential expression.
2. Or align each sample against a common transcriptome (typically the human transcriptome in order to use post-hoc analysis such as GO enrichment analysis)
What do you think ? advices ?