Analyse stranded and non-stranded RNA-seq data together?

Question

[tiago211287]

It is possible to analyse stranded and non-stranded RNA-seq data together? I think it isn't but some people in my laboratory want to, so I came here to get your opinion.

Answer 1

[Istvan Albert]

Of course it all depends on what "together" means. Many tools expect that all data is of one type so those may not support mixing the two types - but that does not mean it would not work.

I think counting reads and adding up the counts separately should work just fine.