To emulate heterogeneous tissue with known and controlled cellular composition, we generated chimeric libraries pooling reads (to a total of 400,000) contributed from the human reference samples (see Additional file 1: Table S2). This process was repeated 720 times, using alternative reference samples to model each cell type. The proportion of reads that the libraries of neurons, astrocytes, oligodendrocytes, and microglia provided to the chimeric libraries varied in predefined ranges (Additional file 1: Figure S3). As a result, each of the chimeric libraries contained reads that followed 32 different distributions (neuronal reads contributed 2–36% of reads, astrocytes 22–76%, oligodendrocytes 6–62%, and microglia 1–5%). Refer to Additional file 1: Table S4 for detailed description of the 32 different distributions. We quantified the chimeric reads using Salmon (v0.7.2) [53] and employed the reference samples that did not contribute reads to the chimeric library as reference panel for the deconvolution methods.
