The Python scripts used to generate and analyze datasets for this article, the simulated data sets, and the raw parameter estimates and their associated uncertainties are available online in the LabArchives respository http://dx.doi.org/10.6070/H4GQ6VQ2.org/10.6070/H4GQ6VQ2
C2Analyzer can also be used to analyze datasets for any organism.
MAGENTA is designed to analyze datasets for which genotype data are not readily available, such as large genome-wide association study (GWAS) meta-analyses.
First, the reads mapped on the simulated exons, i.e. the intron sequences immediately downstream of the un-annotated TE exons, are very rare in the analyzed datasets except for the six ovarian cell line samples.
We were unable to calculate the Hessian matrix for all analyzed datasets, so the results we present for coverage and the median uncertainty for a given sample size are based on the subset of simulated datasets where these estimates were obtained.
Figure 3 shows histograms of the integrated peak intensities from Figure 2, including the optimized GMM configurations obtained following the procedure described on the previous section, the residual errors for the analyzed datasets, and the quantized column thickness assigned to each Gaussian distribution.
For breast-1, ESCC, head-and-neck, lung-2, pancreas-1, and oral-tongue-1, normal and cancer samples were from the same patients (which was not the case for the other analyzed datasets).
Critically, though, for all the analyzed datasets we succeeded in creating conditions where choices were in fact distributed between two options.
It was therefore not necessary to estimate the reassortment rate between HA and SΔNA which is unknown for the analyzed dataset.
The color and shape of nodes are based on different node attributes available for the analyzed dataset.
