RNA-seq: Sequencing data has two coverages

Question

[OST]

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!

[Buffo]

It means that your sample was sequenced twice until they got the coverage that YOU requested. I recommend you to take a look at the read quality (both runs separately), and then decide if combining both runs is a good idea.

Answer 1

[swbarnes2]

I don't think it matters. Unless the differences on coverage are,say, larger than 5x, normalizing will handle that fine. Probably can handle bigger differences than that.