network which is commonly used in image classification and text matching problems.31, 32 We demonstrate the performance using different sets of mixed RNAseq data of pre-acquired purified human and mouse cells. We found the alignment-free method is accurate when assessing a mixed population with relatively equal proportions of human and mouse cells. This method is time efficient and does not significantly increase time for data processing before analysis. However, alignment-based methods outperform the alignment-free approach, particularly when using the “primary alignment” flag in the initial SAM/BAM files.
