Do I still need to add indices (i5 _ i7) to my libraries when using UMIs ?

Yes, the UMIs are random 6 nt sequences that will be added to all samples. Therefore, the UMI sequence cannot be used to uniquely identify the different samples – only to tag distinct random priming events during library generation. The i7 (and i5) indices are added during library amplification and are still required if multiple libraries need to be uniquely barcoded and pooled for sequencing in a single lane or run. The i7 and i5 index sequences are read-out during sequencing during index reads 1 and 2, respectively, and are also required for sample demultiplexing after sequencing. The i7 indices required for the final amplification of QuantSeq libraries are included in every QuantSeq Library Prep Kit. In addition, 12 nt Unique Dual Indices (UDIs) can be added on to enable uniquely dual-indexed libraries for Illumina sequencing. QuantSeq Library Prep Kits and UDIs are available in bundle versions (Cat. No. 113 – 115, 129 – 131).