I am opening this post to ask if I can use the transcript-level assembly obtained with Cufflinks (using a reference genome) to independently quantify the abundance levels of these sequences with RSEM (transcript-level quantification), specifically designed to quantify isoforms. Subsequently, I would perform differential expression (DE) analysis with DeSeq2.
Is this correct? Or should I use the quantifications obtained with Cufflinks for the DE analysis?
Thanks in advance