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