Hi
We've just started using the Illumina Next-Seq platform and haven't been getting good results sequencing our CEL-Seq2 library (75cycle, R1=15bp, R2=77bp), as opposed to what we've been getting previously using Hi-Seq.
QC apparently "looks fine". But I'm not convinced given that the deviation bars in FastQC are huge. %Q30 is ~78%.
The problem is that %mapping to the reference genome is only ~20%, even after discarding sequences with ave Qscore