Experience with whole transcript vs 3' RNA libraries?

Question

[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 insights on the required sequencing depth with 3' end or considerations for data analysis would be very helpful as I’m new to this field.

Thanks!

[ATpoint]

What is the goal of the experiment? New transcripts/fusions, differential tx/genes? Some background would help.