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Old 09-06-2018, 07:11 PM   #1
Junior Member
Location: Australia

Join Date: Sep 2018
Posts: 1
Default What is ERCC spike-in really saying about my sequencing run?

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?

Thank you!
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