Combining Ribozero and PolyA data

[Alessandro1976]

Hi everyone,

I performed mapping and differential expression analysis of PolyA selected RNASeq libraries and now I'm going to get more samples prepared using Ribo-Zero.
Is there a safe way to combine the two datasets and run a new analysis on the extended dataset?

[sarvidsson]

I'd include a few replicates (same RNA sample prepped with both protocols) and see what differences come out.

Why not stick with the same protocol as before?

[Alessandro1976]

Thank you for your answer. Unfortunately the libraries have already been made and it's not possible to include replicates from the previous library. I am only performing the bioinformatics analysis.
So I was wondering if it's possible to combine the two libraries somehow in order to have a bigger set.

[sarvidsson]

I wouldn't be comfortable directly comparing samples with different preparation methods. However, if you're imposing rather high fold ratios when considering differential expression, and will perform downstream validation (e.g. RT-qPCR), I guess you could live with it.