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The ERCC analysis is performed on unaligned data, if the ERCC RNA standards have been added to the samples. There are 92 ERCC spiked-in sequences with different concentrations and different compositions. The idea is that the raw data will be aligned (with Bowtie) to the known ERCC-RNA sequences to get the count of each ERCC sequence. This information is available within Partek^® Flow^® and Partek Flow and will be used to plot the correlation between the observed counts and the expected concentration. If there is a high correlation between the observed counts versus the expected concentration, you can be confident that the quantified RNA-seq data are reliable. Partek Flow supports Mix1 and Mix 2 ERCC formulations. Both formulations use the same ERCC sequences, but each sequence is present at different expected concentrations. If both Mix 1 and Mix 2 formulations have been used, ExFold comparison can be performed to compare the observed and expected Mix1:Mix2 ratio for each spike-in.

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