Partek Flow Documentation

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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
SubtitleTextSummary of ERCC assessment. Each row is a sample (an example is shown)
AnchorNameercc-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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