I have a few questions concerning RNAseq experiment.
we have 10 samples, 5 controls vs 5 Patients. We are going to run them into two lanes. I am wondering how should I index and pool them. Should I use 10 different indexes, pool them all and run in two lanes (that will makes two replicates) or to use 10 different indexes but pull 5 samples in one lane and 5 samples in the second lane that we will have in each pool as different indexes as possible, if so should I run 5 controls in one line and 5 cases in the second line or combine them i.e. 3 controls + 2 cases in one line and 2 controls + 3 cases in the second one.
I hope it is understandable what I wrote.
Thank you in advance.
Thanks Daniel, I would do it in the same way!