We do not recommend multiplexing Lexogen libraries with libraries from other vendors other library types in the same sequencing lane. Though this is possible in principle, specific optimization of index combinations, library pooling conditions, and loading amounts will be required for optimal performance on individual instruments.
...
Due to size differences, libraries prepared with the Lexogen Small RNA-Seq Library Prep Kit (or any other small RNA library prep kit) should not be sequenced together with QuantSeq, CORALL, or LUTHOR , or SENSE HD libraries.
Please refer to the sequencing guidelines for each library type (library adapter details, loading amounts to use, and use of custom sequencing primers, etc.), which are provided in our Library Prep Kit User Guides, and online Frequently Asked Questions (FAQs).