Do I still need to add UDIs to my libraries when using UMIs ?

Yes.

UMIs are unique random sequences (6-nt long) added to each molecule within a same sample during the library generation, prior to library amplification. Therefore, the UMI sequence cannot be used to uniquely identify different samples but only to tag and distinguish molecules within a sample (i.e, distinct random priming events form PCR duplicates).

Learn more about UMIs, their function, and usage in our Lexicon Chapter #8.

Unique Dual Indexes (UDIs - 12-nt long) are added to each sample (i.e., library) during the library amplification. Therefore, each molecule generated from the same RNA sample will have the same index. After sequencing, UDIs help to distinguish molecules between different samples and identify from which samples reads are derived from.

UDIs required for the final amplification of QuantSeq libraries are included as a bundle in every QuantSeq Library Prep Kit (Cat. No. 191 - 196).