Hi Biostar Experts,
For the first time, I'm involved in designing a RNA-Seq experiment for a Illumina HiSeq-2000.
We have 16 samples which we have to divide at only 6 lanes! So is totally clear that we have to multiplex. And we can't use lane 7! or an additional flow cell.
My idea was to multiplex 4 lanes with 3 samples and 2 lanes with 2 samples. 1. Question: Is this a good design? 2. Question: With these design we will get samples with different sample sizes coming from the different sequencing depths. Do you think this a (big) problem for differential expression analyses?
My belief is that the normalizations form DESeq or edgeR are good enough to solve this problem.
Thank's for your help.