Libraries with different size in the same MiniSeq cartridge

Question

[MH85]

Hi everyone,

I have two target seq libraries. They both target the same amplicons (i.e. they have the same primers and adapters). The only difference is that library 1 contains UMIs and thus is 23 bp longer than library 2.

Can I load and sequence these two libraries in the same Illumina MiniSeq cartridge without losing sequencing data from library 1?

Generally, Illumina advises against this as " shorter fragments preferentially bind to the flow cell and thus shorter fragments are overrepresented in the final sequencing data".

However, I am wondering if only 23bp will make any difference? Does anyone have any practical experience with this?

Thanks a lot in advance

Milos

[ATpoint]

I highly doubt it will make a big difference. 23bp is close to nothing. Size bias is from what I know a thing when loading something like ATAC-seq libraries where you have fragments ranging between 200 and 1000bp. 23 is really nothing.