cuffdiff between polyA enriched sample and rRNA depleted sample

Question

[nand]

Hi,

My lab did RNA seq of some samples with just rRNA depletion. Now, there is some RNA-Seq data on GEO that is sequenced after polyA enrichment. Is it possible to cuffdiff my data with the GEO data. At least, is it possible to see differential expression of a list of about 100 transcripts(having poly A tail) I have?

Answer 1

[WouterDeCoster]

Since the library prep of polyA and rRNA depletion is very different, no, that would not be a valid comparison.