I'd like to compare two publicly available datasets that differ in the library prep method, and probably less importantly- read length. I am relatively inexperienced with RNAseq data analysis.
This is the only piece of work I've found that tackles this issue. While I find filtering the reference transcriptome appealing, ratio-based correction seems quite deliberate.
Could the following workflow work?
Filtering the reference transcriptome-> alignment-> counting reads-> DESeq2 +/- sva