I know that in an ideal experiment, one library prep method should be used for all samples.
But I would like to know if it would be possible to use 4 library prep methods/kits on my samples and then send them for sequencing? What differences would there be between the different preparation methods? How would I account for these differences during the bioinformatics analyses?
My samples have varying RIN numbers and concentrations of RNA and so using just one library preparation method/kit would be ideal for some samples, but no good for the other samples, hence why I would need to use 4 methods.
To answer a few of your questions;
1) The RNA was obtained from primary skin cancer samples (Hence the variation in quality and quantity)
2) All library prep methods would produce the same sized libraries for sequencing
3) All the samples are the same type/kind >> Skin cancer_1 marker positive (SC1pos) & Skin cancer_1 marker negative (SC1neg). So far, I have 9 samples (18 total).
4) For the bioinformatics analyses, I would like to generate DEGs for the skin cancer marker positive population (SCpos_vs_SCneg)
Thank you very much in advance!