I've used ERCC spike-in to prep the library for my recent run of sc-RNA seq.
Looking at the plot of ERCC read counts vs ERCC concentration, I know we should ideally expect to see a nice correlation with R2 =1, for every sample in the library.
Looking at the sequences itself, QC and mapping %, I've had a bad run. Slopes of the ERCC plot are all over the board and anywhere from 0 to 1.
What specifically does this ERCC plot really indicate about the sequencing run? Besides that "something went wrong" or that samples aren't evenly amplified? - How should I rectify this?
While we're at this, can someone explain or point me to a good resource on how to use ERCC counts to normalise my data?