Sequencing data has two coverages

Hello!

I want to kindly get an input on a predicament we are facing. Our RNA Bulk-seq data has arrived and this is the note we got: “Your plate was originally sequenced however had low coverage and so the group resequenced and has included both runs to ensure coverage was met”

This means we have two coverages for our RNA-seq data: one with high coverage, and one with low coverage.

What should we do in this scenario? The data from one coverage seems different from the other coverage so far. Does this make sense? Do we use one coverage, combine, etc? Any help or advice is greatly appreciated!