Experience with whole transcript vs 3' RNA libraries?

[kiruseq]

Hi,
I’m planning a large RNAseq project and I’m currently weighting the pros and cons of different library preparation protocols, specifically Lexogen’s 3’ mRNA Quant-seq kit vs. Illumina’s Truseq stranded mRNA. I’ve found some articles comparing whole transcript and 3’-end library prep methods but I’m wondering if anyone has personal experience to share on that matter. Especially any considerations for the data analysis would be helpful as I’m new to this field.

Thanks!

Edit:
I'm mainly interested in DEG, so I'm not concerned about losing splicing info with the 3' method.

[luc]

In our experience Quantseq seems to perform better than other 3' tag-seq methods that rely on tagmentation for adding the 5' adapter. We do not have hard data, though.