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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 96 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.

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Numbered figure captions
SubtitleText Summary of ERCC assessment. Each row is a sample (an example is shown) AnchorName ercc-table

The ERCC spike-ins plot (Figure 3) shows the regression lines between the actual spike-in concentration (x-axis, given in log2 log₂ space) and the observed alignment counts (y-axis, given in log2 log₂ space), for all the samples in the project. The samples are depicted as lines, and the probes with the highest and lowest concentration are highlighted as dots. Regression line for a particular sample can be turned off by simply clicking on the sample name in the legend beneath the plot.

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