DTU by combining different type of RNA seq data

Question

[aimanbarki]

Hello , I am working with some human data from ncbi. I was able find 5 (2 controls + 3 other group) samples which are unstranded polyA plus and 4 ((2 controls + 32other group) samples are Total RNA – Strand-specific (reverse). Is there any way I can use them in one DTU analysis (Hisat2- DEXSeq) or if I used them what are the precautions I need to take?

Answer 1

[Trivas]

I think you could implement batch correction (RUV, combat) to account for sample prep differences.