How to compare rRNA-depleted and polyA enriched RNAseq datasets ?

Question

[masaver]

Hello Everyone,

I'm interested in comparing two RNAseq datasets from breast normal & tumor tissue. The problem is that one of them generated with rRNA depletion, while the other was generated through polyA-enrichment.

Would anyone know an appropriate way to compare/integrate these two types of data sets ?

Thanks in advance for the help.

Best,

-M,

[h.mon]

Normal and tumor are perfectly confounded with rRNA depletion and poly-A selection, so you can't untangle the effects you are interested (tumor vs normal tissue) from the ones you are not interested (rRNA depletion vs poly-A enrichment).